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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaaaaaatattcctgaaaatgagtattttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG

Basic information

species Glycine max
transcript GLYMA07G00420.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 5
gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcat----tcataaaaaaatatt------cctgaaaatgagtattttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
               |   ||  |  || |  | | ||| | |||  || |     |  | || | | |    || | |  |  | ||      | | |       | ||| |  ||||||| ||  | ||||| ||||| || ||||| |||| |||||| || ||||||||||||||| |||| |||||||| |||||||||||||| |||||||| |
--------------gtaagtggcaatcacttcttttttttttctgcaagcagcagagttcatgctacttcatctcgtcatcagttctttagttacttaatcgcatctttttctcctgcagTCCCGCTTTGATATCTTGAAGATTCATTCAAGAAAAATGAACTTGATGCGTGGCATTGATCTGAAAAAGATTGCAGAGAAGATGAATGGGGCATCTGGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 7
gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaaaaaatattcctgaaaatgagtattttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
               |   ||||    | | |  | | | |  |  | |  ||  |   | || |   ||      |  ||   | |         | ||||   | ||||| ||  | ||||| ||||| || ||||| |||| |||||| || |||||||| |||||| |||| ||||| || || ||||||||||| || || || |
--------------gtaagtgctgataacttac-tgtatattgtttgtgttaatttttccatgatttcttgtgttgatgatgcgctta--------tcttttgctttcagTCACGCTTTGATATCTTGAAGATTCATTCAAGAAAAATGAACTTGATGCGTGGTATTGATCTGAAAAAGATCGCTGAAAAGATGAATGGGGCTTCAGGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 7
gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaaaa-aatattcctgaaaatgagt---atttttta----tgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
                                ||| ||||             | |  ||||| ||  || | |     | |  | |||| |  | |    || ||||     ||||||| ||  | ||||| ||||| |||||||| |||| |||||| || ||||||||||||||| |||| ||||| || || ||||||||||| || || || |
-------------------------------gtatgtttggctaactcatcctgttatacctgttgattttacatggctactgctgctgacagggcgcttaatcttttgcccttgcagTCACGTTTCGATATCTTGAAGATCCATTCAAGAAAAATGAACTTGATGCGTGGCATTGATCTGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------------------gtttgcatttttgct---ttcatgctacccattaatatatt-tgtactgggagaaaagat-------gcacctggtgcattcataaaaaaatat-----tcctgaaaatgagtattttttat-------gcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
                                                     | |||  ||||||   | | |  |      |||  |||  | ||||| |  |||   |         || |  || |  || |   |   |      |   |  ||||  ||||| | ||       |||||| ||  | ||||| ||||| || || || || | ||||||||| |||||||| || ||| |||| |||||||| |||||||||||||| || || ||||
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------------------------------------------------------------gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaaaaaatattcctgaaaatgagtatttttta-------tgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
                                                                                   || | ||||   || ||||  | |    ||| | | || | ||        | |  ||  |    ||        |  |   |   |  ||||  | |||   |       ||||||| ||  | || || ||||| || || || || | ||||||||| |||||||| || ||| |||| |||||||| |||||||||||||| || || ||||
gtaatacttgtgctctgagaaaatgatattgactgttgtttttggtgatatgaatacattattcgtcaaagtaggcaccttatttagtatttagactatcat-ttgcagcataaaaaactt-ttctttatctccatactcattttactcaagtgaggcaggacggtttggctaatgtatgtttccaaaatgtgttgcagTCACGTTTTGACATCTTGAAGATTCACTCGAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGCGCTTCAGGTG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 7
gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgc-acctggt--gcatt-cataaaaaaatattcctgaaaatgagtattttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
       || | | ||| | | ||     | || |   | | |||| ||  | | ||| | |||    ||||| |||| |  ||   |  | |   |  | |||    |  ||||||||   ||||||||| ||||| || || || | ||||||||| |||||||| || ||| ||||||||||||| |||||||||||||| ||||||||||
------gttatggtttttaggatatg---tgatttgact-ttctggtagctatgttgctatctgactggcattgcatatattaaagatttttattttttgaatt----actcagTCTCGCTGGGATATTTTAAAAATACACTCGAGGAAAATGAATTTGATGCGTGGGATCGATCTGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 7
gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaa-aaaatat-tcctgaaaatgagtatt--ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
                | ||| |    | |   |||||  | |||  |    |  |     |      | || |    ||  |  | ||||   |   | ||  |||| | ||||| ||  | ||||||||||||||||| || |||| |||||| ||||||||||| |||||| |||||||||| || |||||||||||||| ||||||||||
--------------agttatgattataaattcgatattcattctgatatggcatttttttttatcaactgcaaaggtgaagcacatgctgatttttttttttcttttttttcagTCCCGCTTTGATATTTTGAAAATCCACTCAAGAAAAATGAACTTAATGCGTGGGATTGATCTGAAGAAGATAGCAGAGAAGATGAATGGTGCATCTGGTG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaaaaaatattcctgaaaatgagtatttt-ttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
                |||  | |||  | ||    ||  ||     |    |    ||        |  |   | | |  | ||             |  |  | |||| |   || ||| |||||||||  |||| ||  | ||||| ||||| || |  ||||| |||||||| || |||||||||||||||||||| || ||||||   || |||||||| |
gtatacaaaggcgtgatttataatttgccatttcctctctcccaccttgctctctcgctcctttcttattttt-cttcgccccttgtcttgtgtgagctaatctatatgattgccttgttacgcagTCTCGATTGGACATCCTTAAAATTCATTCAAGGAAGATGAACTTAATGCGAGGTATTGATTTGAAGAAGATTGCTGAAAAGATGGGAGGCGCATCTGGAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 2
gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaaaaaatattcctgaaaatgagtattttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
    | | |      |  ||  |     || |  | ||| | ||         |||   ||  ||   |   | |    || ||  ||   |     || |  | ||||||||||  |||||||| | ||||| ||||| ||||  |||||  | ||||| || |||||||||||||| ||||| |||||||||   || ||||| || |
----gtactcaaaagtgtataatcttagttta-gtttttttgcttt------tgattttccctgttattgtgtgagcttatctttatggtta-----atctggtgtgcagTCTCGATTGGATATTCTCAAAATTCATTCAAGAAAGATGAACCTCATGCGAGGTATTGATTTGAAGAAAATTGCTGAGAAGATGGGAGGTGCATCAGGGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|214009603|gb|DB988312.1|DB988312
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|37995024|gb|CF806613.1|CF806613
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|193564595|gb|FK521432.1|FK521432
EST:     AAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: AAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|192332825|gb|FK026826.1|FK026826
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCCGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|192332826|gb|FK026827.1|FK026827
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCCGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|17022699|gb|BM093733.1|BM093733
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|254318622|gb|GR832790.1|GR832790
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|193421449|gb|FK389622.1|FK389622
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCG
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCG
EST: gi|193404796|gb|FK369625.1|FK369625
EST:     AGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCG
genomic: AGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATA-TTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCG
EST: gi|207714550|gb|GD696995.1|GD696995
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|16277739|gb|BI942538.1|BI942538
EST:     GACCATGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|209727795|gb|BW658719.1|BW658719
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|16344411|gb|BI970006.1|BI970006
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|16344478|gb|BI970073.1|BI970073
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|254318623|gb|GR832791.1|GR832791
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|15589592|gb|BI674208.1|BI674208
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
EST: gi|7924399|gb|AW830425.1|AW830425
EST:     GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG                         TCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT
genomic: GACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAGgtttgcattt ... ttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacctggtgcattcataaaaaaatattcctgaaaatgagtattttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG
                                         tatttttt  CT-rich tract
                ataaaaaaatattcct  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcatttttgctttcatgctacccattaatatatttgtactgggagaaaagatgcacctggtgcattcataaaaaaatattcctgaaaatgagtattttttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA