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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttag

Basic information

species Glycine max
transcript GLYMA07G05220.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 7
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagact-cgtcctctagcttttttttatca-ttgtttcca-tgaaaataaatc-atttgactaaaat-tttctcatttttag------------------
||| ||| | || |||||||||||||| | || ||||| |||||| ||||||| |||||||||||||| ||||| ||||||| || ||| ||||||||||| || ||| | | | || | |||||| || | | || | ||| | || |||||| | || ||||| | |
GGCCAATCGTACAGATGCTTGTTTTATCCGTGTAATTGGCAGTGAGTTAGTTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgta---tgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttag

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatca-----tttgactaaaattttctcatttttag
|| || |||||||||||||||| || | || ||||||||||||||||||||||| |||||||| || || ||| ||||||| | ||||| || |||||| | | | | | || || | || ||| | || | | | | | | ||| ||| | | ||| |
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtata-tctagggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag-

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatca-----tttgactaaaattttctcatttttag
|||||||||||||| || | || ||||||||||||||||||||||| |||||||| || || ||| ||||||| | ||||| || |||||| | | | | | || || | || ||| | || | | | | | | ||| ||| | | ||| |
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATA-TCTAGggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag-

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 7
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaat----catttgactaaaattttctcatttttag---
|| ||| |||||||||||||||| || | || |||||||||||| |||||||||| ||||| || || || ||| ||||||| | ||||| || |||||| | | | | || ||| | || | || | ||| |||| | | | ||| | || |||| || | | | |
AGCAAATCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGTTAGTTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgta---tatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtag

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 7
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgt---aaaatgcacaagactcgtcctctagcttttttt-tatcattgtttccatgaa--aataaatcatttgactaaaattttctcatttt-tag
|||||| || |||||||| |||||||| | |||||||||||||| || ||||||||||| ||||| ||||||||||||||||||||||||||||||||||| || ||| | | | | ||| ||| | | |||||| | || || | |||| | || | | | ||
GGCTAACAGAACTGATGCATGTTTTATTCGTGTTATTGGAAGTGAACTTGTTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcag

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 7
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttt--tttatcattgtttccat---gaaaata------aatcatttgactaaaattttctcatttttag-
|| |||||||| |||||||| || || | |||||||| |||||||| |||||||||||||| || ||||| ||| ||||||| ||||| || || |||| || | | || | | | ||| || |||| || || | || | ||||| | || || | | | |
TGCCAATAGGACAGATGCTTGCTTCATTCGTGTTATTGGCAGTGAGCTTGTTCAGAAATATGTAGGAGAGGGTGCTCGGATGGTCCGTGAGCTTTTCCAGgcaagtcaatcgttaatcacttcacatccctgaggtttgatatggtttggatttagagactatcctttagtcattcgcctggaacctgtatactcacatc

upper sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 7
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttt--tttatcattgtttc-catgaaaataaatc--------atttgactaaaa--ttttctcatttttag
|| |||||||| ||||| || || || | |||||||| |||||||| |||||||||||||| || ||||| ||| | ||||||||||| || |||||||||| || || || | | |||| |||| || | || | | ||| || ||||| | ||| | || ||
TGCAAATAGGACAGATGCATGCTTCATTCGTGTTATTGGCAGTGAGCTTGTTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagatacatggtgatctctccgcatctttcagatttaagatgggttggcgttaaagaggattccaagagaatttgccagaaaagctacgccaagcgta-

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|19937368|gb|BQ081261.1|BQ081261
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|16277271|gb|BI942294.1|BI942294
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|57575942|gb|CX548913.1|CX548913
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|16346898|gb|BI972493.1|BI972493
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGNTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|58024535|gb|CX711276.1|CX711276
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|209717333|gb|BW659036.1|BW659036
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|58021578|gb|CX708319.1|CX708319
EST:     TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG