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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag

Basic information

species Glycine max
transcript GLYMA10G30400.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 5'ss of exon 3
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttt-tttag
||| || |||||||| ||||| || || ||||||||||| || ||| | |||||||| || ||| ||||||| || ||||| ||||| ||||||||| ||   | |       |||  ||  |      || ||  |   ||||   | |   |   | | |   ||   || | || | |||  | |  ||
GTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAGgtttgtccatca------aaataattttag--gctttagtgttatgtttt---agtaaaaccagaagttgatttcctactgttttaactactgtccag

upper sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G124434_T01 (Zea mays), 5'ss of exon 3
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag
||| || |||||||| ||||| || || |||||||| || || ||| | || || ||||||||||||||||| || ||||| ||||| ||||||||  |||  |     |   |    |    ||  |||| |||    || |  ||| |   ||     | |||    |   | ||  |     ||| ||
GTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAGgtgtgttcatcgaaatacaa----tgacgttcctgtttgttagacatatatacagtcaaatc----taaatcccctcggtgttacg-----tttcag

upper sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 3
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTA---ATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag
||| |||||||| || |||||||||||||| || || ||||| |||||||| ||||   ||||||||||||||||||| ||||| ||||| || |||||| || | | || ||||  || ||||  ||  |   | ||  ||| | |    ||  |    |  || ||     | || | |             
GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGgtttgt-gattattttttatat-gttc--ttgctaaagatttatgagtcttttcttatgtgatgttttgatgc---tgatatag-------------

upper sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ36458 (Selaginella moellendorffii), 5'ss of exon 2
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag
 ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||||       |||       ||  |   ||   | | |   ||||   |||  |   |    ||  |  || |||    | ||||             
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAGgt------atga-------aaacgaaaaaaaaaagct---tcttttcttttgcggggaatctgaaaaaaaattgc---actttgcag----------

upper sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ19598 (Selaginella moellendorffii), 5'ss of exon 2
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag
 ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| |||||||||||||| || ||       |||       ||      ||   |      |||||   |||      || ||  | |  ||||||    | ||||             
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAAgt------atgaa-----aaagaaaaaaaaaaaaaaaacttcttctcttttgtgg-ggaatctgaaaaaatttgc---actttgcag----------

upper sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ10353 (Selaginella moellendorffii), 5'ss of exon 2
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag
 ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||||       |||       ||      ||   |    | |||||   |||  |   || ||  | |  ||||||    | ||||             
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAGgt------atga------aaaagaaaaaaacaaaaaagcttcttttcttttgcgg-ggaatctgaaaaaatttgc---actttgcag----------

upper sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ18599 (Selaginella moellendorffii), 5'ss of exon 2
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag
 ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||||    ||   |      |||      ||   |    |||||||   |||      |    |   |  || |||    | ||||             
ATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAGgta---tgaaaaa-----gaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgc---actttgcag----------

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|6566810|gb|AW234442.1|AW234442
EST:     AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG                         CCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAG
genomic: AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggt ... ctttttttagCCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAG
EST: gi|15814341|gb|BI786616.1|BI786616
EST:     AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG                         CCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAG
genomic: AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggt ... ctttttttagCCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAG
EST: gi|19347182|gb|BM892062.1|BM892062
EST:     AGTTGGAAACTAATGTGAGCTTGAAGGAATCCGATGCATGGCCAACTGAG                         CCTCAAGATGCATATGGGCTAGAGAAA
genomic: AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggt ... ctttttttagCCTCAAGATGCATATGGGCTAGAGAAA
EST: gi|19348759|gb|BM893291.1|BM893291
EST:     AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG                         CCTCAAGATGCATATGGGCTAGAGAAA
genomic: AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggt ... ctttttttagCCTCAAGATGCATATGGGCTAGAGAAA
EST: gi|26058273|gb|CA801187.1|CA801187
EST:     AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG                         CCTCAAGATGCATATGGGCTAGAGAAA
genomic: AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggt ... ctttttttagCCTCAAGATGCATATGGGCTAGAGAAA
EST: gi|151403142|gb|EV272952.1|EV272952
EST:     AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG                         CCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAG
genomic: AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggt ... ctttttttagCCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAG
EST: gi|20813404|gb|BQ297882.1|BQ297882
EST:     AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG                         CCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAG
genomic: AGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggt ... ctttttttagCCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAGgttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA