BLASTN 2.2.26+
Reference:
Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
"A greedy algorithm for aligning DNA sequences", J Comput Biol 2000;
7(1-2):203-14.
Database: TAIR10_cdna_20110103_representative_gene_model_updated
33,602 sequences; 51,074,197 total letters
Query= Ahg485852
Length=2291
Score E
Sequences producing significant alignments: (Bits) Value
AT3G54500.3 | Symbols: | FUNCTIONS IN: molecular_function unkn... 2974 0.0
AT3G54490.1 | Symbols: RPB5E | RNA polymerase II fifth largest ... 91.6 3e-17
> AT3G54500.3 | Symbols: | FUNCTIONS IN: molecular_function unknown;
INVOLVED IN: biological_process unknown; LOCATED IN:
cellular_component unknown; EXPRESSED IN: 22 plant structures;
EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana
protein match is: dentin sialophosphoprotein-related (TAIR:AT5G64170.1).
| chr3:20175370-20179027 REVERSE LENGTH=2639
Length=2639
Score = 2974 bits (1610), Expect = 0.0
Identities = 1789/1872 (96%), Gaps = 26/1872 (1%)
Strand=Plus/Plus
Query 442 AGAGAAAACGTCTGAACTTGGGAAAGGCCCTGATATTTTTCATAGCTCTGATGAGAGTAA 501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 740 AGAGAAAACGTCTGAACTTGGGAAAGGCCCTGATATTTTTCATAGCTCTGATGAGAGTAA 799
Query 502 AGAGCAAGGTGATTTTGATGACTACAGCTGGGCCAACATTGGTAGTTTTGATGATCTTGA 561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 800 AGAGCAAGGTGATTTTGATGACTACAGCTGGGCCAACATTGGTAGTTTTGATGATCTTGA 859
Query 562 TCGAATGTTCAGCAATGATGTCCCTATATTTGGCGATAGCAGTCTCAGCGGTGGTGATGA 621
||||||||||||||||||||||||||||||||| ||| ||||||||||||||||||||||
Sbjct 860 TCGAATGTTCAGCAATGATGTCCCTATATTTGGTGATGGCAGTCTCAGCGGTGGTGATGA 919
Query 622 GTTATGGTCTTCTTCTAAAGATGTTTCCAATAGCCCAAAATCATTATCATCAATGTTGGA 681
||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct 920 GTTATGGTCATCTTCTAAAGATGTATCCAATAGCCCAAAATCATTATCATCAATGTTGGA 979
Query 682 CTCTCAAGATCTAGGATTGGATATTAGAACTGAGTTTGAGCAACAAGAGAACCAGCAATT 741
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 980 CTCTCAAGATCTAGGATTGGATATTAGAACTGAGTTTGAGCAACAAGAGAACCAGCAATT 1039
Query 742 TCCATTGACTGGAAAAGCCAATGGTCCGTCATCCCAAAGTGTGCCGAGTCTACGTGTAAC 801
|||||||||||||||||||||||||| ||||||||||||||| || ||| ||||||||||
Sbjct 1040 TCCATTGACTGGAAAAGCCAATGGTCTGTCATCCCAAAGTGTCCCAAGTGTACGTGTAAC 1099
Query 802 TCTAAAGGCTGACCAATATCGTGAGCATAAGGGTCAACCCTCAGTTGAGGACCAGCCATA 861
||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1100 TCTTAAGGCTGACCAATATCGTGAGCATAAGGGTCAACCCTCAGTTGAGGACCAGCCATA 1159
Query 862 TCAACAAAATAAAATGATGAAGTTTTCGAAAATGCCTGGGACTTCTGAGGCATGGGCATT 921
|||||||||||||||||||||||||||||||||||||||||||||||||||| || | ||
Sbjct 1160 TCAACAAAATAAAATGATGAAGTTTTCGAAAATGCCTGGGACTTCTGAGGCAAGGCCCTT 1219
Query 922 TCATGAGCTGTACGGTCAGAGGATTCCATCTAGTAATTCTCCTGGAAAGT-TGGTAAATC 980
||| ||||||||||||||||||||||||| ||||||||| ||||||| | || ||||||
Sbjct 1220 TCAAGAGCTGTACGGTCAGAGGATTCCATTTAGTAATTCAGCTGGAAAATGTG-TAAATC 1278
Query 981 AGTTGACACCGCCACGATCTTCTCTGATGGCTGTTAATCTGCAGAGTGAGTCTGAAGGAT 1040
||||| ||||||||| ||| |||||||||||||||||||| | |||||||||||| || |
Sbjct 1279 AGTTGGCACCGCCACAATCGTCTCTGATGGCTGTTAATCTCCTGAGTGAGTCTGAGGGGT 1338
Query 1041 CTGGGACATCACACTATTCACATATGCCAAACCAATACATGGCTACTTCTGCTTTTGGTA 1100
||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct 1339 CTGGGACATCACACTATTCACATATGCCAAACCAATACATGGCTAATTCTGCTTTTGGTA 1398
Query 1101 ATCTTGCAAATCCATATTCTAGTGTGCCTGTAATTTCGGCCGTCCAACATCCTGATGTTA 1160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1399 ATCTTGCAAATCCATATTCTAGTGTGCCTGTAATTTCGGCCGTCCAACATCCTGATGTTA 1458
Query 1161 AGAATCAGTTGATGCATCCTTCTTACAATCCTGCTACTGCTACCTCCGTAAACATGGCAA 1220
||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||
Sbjct 1459 GGAATCAGTTGATGCATCCTTCCTACAATCCTGCTACTGCTACCTCAGTAAACATGGCAA 1518
Query 1221 CAGATGCCTCTGCACGGCCTTCAACAATGACACCACAGGAAAAACTAGAAAAACTTAGAC 1280
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1519 CAGATGCCTCTGCACGGCCTTCAACAATGACACCACAGGAAAAACTAGAAAAACTTAGAC 1578
Query 1281 GCAGACAGCAAATGCAGGCAATGCTTGCCATTCAAAGACAACAGAAGCAATTTTCTCATC 1340
|||||||||||||||||||||||||||||||||| ||||||||| |||||||||||||||
Sbjct 1579 GCAGACAGCAAATGCAGGCAATGCTTGCCATTCAGAGACAACAGCAGCAATTTTCTCATC 1638
Query 1341 AGGTGCCTGTAGCAGATCAATCCATTACTCAAAACTGTCTCCAAGATATTCCACTCCAGC 1400
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1639 AGGTGCCTGTAGCAGATCAATCCATTACTCAAAACTGTCTCCAAGATATTCCACTCCAGC 1698
Query 1401 TTGTCGACAAAACTAATATCCAAGGGCTAACTGCAATGCCTTCCTTTGATCCTAGTTCAT 1460
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Sbjct 1699 TTGTCGACAAAACTAATCTCCAAGGGCTAACTGCAATGCCTTCCTTTGATCCTAGTTCAT 1758
Query 1461 CTTTGGAACAAGATGATTCTGGCAAATTTGCTGCTGCTGTTGATAATTCAGCAGAATTCT 1520
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1759 CTTTGGAACAAGATGATTCTGGCAAATTTGCTGCTGCTGTTGATAATTCAGCAGAATTCG 1818
Query 1521 CAGTTCTTTATCGGCTTCAGGATGTTGTAGCAAAGTTGGATATGGGAACACGGACTTGTA 1580
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1819 CAGTTCTTTATCGGCTTCAGGATGTTGTAGCAAAGTTGGATATGGGAACACGGACTTGTA 1878
Query 1581 TACGGGATAGCTTATTCCGGCTGGCTGGTAGCGCAGCTCAGAGACATTACACTAGTGATA 1640
|||||||||||||||||||| |||||||||| ||||||||||||||||||||||||||||
Sbjct 1879 TACGGGATAGCTTATTCCGGTTGGCTGGTAGTGCAGCTCAGAGACATTACACTAGTGATA 1938
Query 1641 CAGCCCACAGTAACAAGACTAGCCAGGATGAGCAGGAAGTTATTCCCAGAGAAGAATCCA 1700
|| |||||||||||||||||||||||||||| |||||||| |||||||||||||||||||
Sbjct 1939 CATCCCACAGTAACAAGACTAGCCAGGATGACCAGGAAGTCATTCCCAGAGAAGAATCCA 1998
Query 1701 GATATAGATATGCTGGGATGCCAGATACAGAAGCAGTGACCAACCCCACAGACAGAACTG 1760
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1999 GATATAGATATGCTGGGATGCCAGATACAGAAGCAGTGACCAACCCCACAGACAGAACTG 2058
Query 1761 TGGCTCATTTGCTCTTTCATAGGCCTTTTGATATGTTGGCGGCAAAGCGTATGGAAGGAC 1820
||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Sbjct 2059 TGGCTCATTTGCTCTTTCATAGGCCTTTTGATATGTTGGCGGCAAAGCGAATGGAAGGAC 2118
Query 1821 CAGAATCACCCGCTTCTTCGAAGATGGGAACTGAAGAAAAAGGGAATTTTCCTAAATGCA 1880
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 2119 CAGAATCACCCGCTTCTTCGAAGATGGGAACTGAAGAAAAAGGGAATTTTCCTAAATGCA 2178
Query 1881 TCATACGAGAGACTCACTTAAATAAGCAGAAAGCTCAAAAGGAAGAAGGACCTGCAGATT 1940
|||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct 2179 GCATACGAGAGACTCACTTAACTAAGCAGAAAGCTCAAAAGGAAGAAGGACCTGCAGATT 2238
Query 1941 TACTTGCTTTGGGGAATGCACCCAACTCTGGATCCAGTAGTACTGTTGGTGAGAGGGTTG 2000
||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct 2239 CACTTGCTTTGGGGAATGCACCCAACTCTGGATCTAGTAGTACTGTTGGTGAGAGGGTTG 2298
Query 2001 TTGAAGCATCCCAAGGAAACAAAAGAAAGTTGTGAAAATTAGAAGTTTAGGTTGCCGTGT 2060
|||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||
Sbjct 2299 TTGAAGCATCCCAAGGAAACAAAAGAAAATTGTGAAATTTAGAAGTTTAGGTTGCCGTGT 2358
Query 2061 TAGAGAGGAGCTTTGGGAATTTCAGCAGACTAGACAACATCTCTCTGCGTCCCTTGAAAC 2120
||||||||||||||||| ||||| |||||||||||| ||||| |||||||| ||||||||
Sbjct 2359 TAGAGAGGAGCTTTGGGTATTTCTGCAGACTAGACAGCATCTTTCTGCGTCTCTTGAAAC 2418
Query 2121 AATCTCCTCATTGCTCCTTTCTTGT-AA--T-T-A-----G-A-tt---ttttttt---- 2161
|||||||| | |||||||||||||| || | | | | | || |||||||
Sbjct 2419 AATCTCCTGACTGCTCCTTTCTTGTGAAGCTCTTATTCTTGTAATTAGATTTTTTTTTTT 2478
Query 2162 --GTTACTTTTCAAAAACCTCTTTTGTTACACGTACCTCCATGACAACTACATTTTGGAA 2219
|||||||||| |||||||||||||||| ||||| ||||||||||||||||||||||||
Sbjct 2479 TTGTTACTTTTCGAAAACCTCTTTTGTTATACGTATCTCCATGACAACTACATTTTGGAA 2538
Query 2220 AACTCGTGTAGTTTGCAATGtttttttCCTCATTCAAAACCAGATTCAATCTCTTAATAC 2279
||| |||||||||||||||||||| || ||||| ||||||||||||||||||||||||
Sbjct 2539 AAC--GTGTAGTTTGCAATGTTTTTCCCC-CATTCGAAACCAGATTCAATCTCTTAATAC 2595
Query 2280 AATTGTAAGCAC 2291
||||||||||||
Sbjct 2596 AATTGTAAGCAC 2607
Score = 407 bits (220), Expect = 3e-112
Identities = 372/437 (85%), Gaps = 44/437 (10%)
Strand=Plus/Plus
Query 38 AGCTGGCGATGTGTGGAGCAATTC-GGGAGCGTGATATAGGTTCTTTGATTCGATTTTGT 96
||||||||||||||||||||| || |||||| |||| | || ||| ||||||||||||||
Sbjct 222 AGCTGGCGATGTGTGGAGCAA-TCAGGGAGCTTGATTTTGGGTCTGTGATTCGATTTTGT 280
Query 97 TTCTCAAGTCATGTTTGATTGGGAAGAAGAAGAGCTTACTAATATGATATGGGGTGATGA 156
||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 281 TTCTCCAGTCATGTTTGATTGGGAAGAAGAAGAGCTTACTAATATGATATGGGGTGATGA 340
Query 157 CGGTGAGACAGGCGACCATATTGTGCCTTTTAAA--CA-A------C---TTAATAAGAA 204
| ||||||||||||||||||||||||||||||| || | | |||| || ||
Sbjct 341 TGCTGAGACAGGCGACCATATTGTGCCTTTTAAAGTCAGAAGTGAACAACTTAACAAAAA 400
Query 205 GGAACAGAGTGAAGAATCTAAGACTGCTAAACTGGCTGAGCAAAAGATAACTGGGACTAA 264
|||||||| ||| ||||||||||| | | |||||||||||||||||||||||||
Sbjct 401 GGAACAGATTGAGGAATCTAAGAC----A----G-CTGAGCAAAAGATAACTGGGACTAA 451
Query 265 AACTGACCTCCATGATGATAAATT-GGGGAGCAGTTC-AGGCCATAATGTTGATGACGGG 322
|| ||||||||||||| | ||||| |||||||||||| || ||||||||||||||| |||
Sbjct 452 AATTGACCTCCATGATAA-AAATTTGGGGAGCAGTTCGAG-CCATAATGTTGATGAGGGG 509
Query 323 ACT-CCTCAGCCAGATTTCTGTATGAGCTCATGGTCTGAC---TC-C-A-C-AA----A- 369
|| |||||||||||||||||||||||||||||| ||||| || | | | || |
Sbjct 510 -CTTCCTCAGCCAGATTTCTGTATGAGCTCATGGCCTGACACGTCGCTAACTAATGCTAC 568
Query 370 A--GCT-GATCCAGATTTGAGGGCGACTCAACTTTCAAAATGCTTAGCTGAGCCAGCCAG 426
| | | |||| ||||||||| |||||| ||||||||||||||||||||||||||| |||
Sbjct 569 AAAGGTTGATCAAGATTTGAGTGCGACTGAACTTTCAAAATGCTTAGCTGAGCCAGTCAG 628
Query 427 ATATGATTCAACAAGAG 443
|||||||||||||||||
Sbjct 629 ATATGATTCAACAAGAG 645
> AT3G54490.1 | Symbols: RPB5E | RNA polymerase II fifth largest
subunit, E | chr3:20173619-20175462 FORWARD LENGTH=921
Length=921
Score = 91.6 bits (49), Expect = 3e-17
Identities = 58/62 (94%), Gaps = 1/62 (2%)
Strand=Plus/Minus
Query 2230 GTTTGCAATGtttttttCCTCATTCAAAACCAGATTCAATCTCTTAATACAATTGTAAGC 2289
|||||||||| ||||| || ||||| ||||||||||||||||||||||||||||||||||
Sbjct 921 GTTTGCAATG-TTTTTCCCCCATTCGAAACCAGATTCAATCTCTTAATACAATTGTAAGC 863
Query 2290 AC 2291
||
Sbjct 862 AC 861
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 113704234425
Database: TAIR10_cdna_20110103_representative_gene_model_updated
Posted date: Sep 25, 2014 6:13 PM
Number of letters in database: 51,074,197
Number of sequences in database: 33,602
Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5