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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgattgatattgtatcaataaaaatctgacattcgaatactgtattaggagatttgctttactgcattaaatatctatttctttttataatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG

Basic information

species Glycine max
transcript GLYMA06G42840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 1
ttatgattgatattgtatcaataaaaatctgacattcgaatactgtattaggagatttgctttactgcattaaatatctatttctttttataat-----ttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG
 |   | | ||    |  || ||||    || |||    || |    ||     | ||| |  |     || ||| |||||     | | | |      |||||||| ||||| ||  |||| |||||||| ||||| || |||||||| || || || ||||| || |||||||||||||| || ||||| || |||
-ttgaaataatcggatg-cagtaaatgcttgccatctctattccaccttgt---agttgatcaaaatagtttaatgtctatactaatatgtgaggtggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAG

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 1
-ttatgattgatattgtatcaataaaaat--ctgacattcgaatactgtattaggagatttgctttactgcattaaatatctatttctttttataatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG
  ||     ||      |  |||    |   ||  | |||      ||||  |  ||| | | ||||   | |  ||||  ||| |     | | ||||  |||| ||||| ||| |||| || || || |||||||| ||||| || |||||||| || || |||||||||||||||||||| ||||||||||||
tatacatcggaggaaacactaattgttactactttccttcattctttgtag-acaagaatagttttaactcctgtaataa-tatgttcacgtttgattt-tagGAAATGTCTGCTGCTGTTATAGAAGGAAATGATGCTGTTACCGGTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAG

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 1
-ttatgattgatattgtatcaataaaaatctgacattcgaatactgtattaggag-atttgctttac-tgcattaaatatctatttctttttataatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG
 |||  | |   |   || |||||   |   ||   ||  ||     || |   | || |  ||| | |  |||  ||  ||||  |||  | | | |||||||| ||||||||| |||| ||||||||||||||| | || ||||| || ||||| |||||||| ||||||||||||||||| || |||||||||
tttagaaatagcagc-tagcaatagggaa--gattatcctatttgacataattggcatgtattttgcatttattttattcctatgacttgatgtgaattgcagGAAATGTCAGCTGCTGTTATTGAGGGGAATGATCCAGTCACTGGTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG

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|193660453|gb|FK603111.1|FK603111
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCA
EST: gi|208215639|gb|GE013769.1|GE013769
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|120530050|gb|EH258184.1|EH258184
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|37996099|gb|CF807688.1|CF807688
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|193416669|gb|FK384125.1|FK384125
EST:     CTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: CTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|120531619|gb|EH259752.1|EH259752
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|193561375|gb|FK518172.1|FK518172
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCA
EST: gi|5058337|gb|AI736813.1|AI736813
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|208268482|gb|GE069393.1|GE069393
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|193433005|gb|FK395713.1|FK395713
EST:     AAGTTCCTCGCCGGAGCNCCGATACGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGGTGCCGTTACTGGCCACATA
genomic: AAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
EST: gi|42723166|gb|CK769065.1|CK769065
EST:     AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAG                         GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA
genomic: AGCCGCAACCCGAAGTTCCTCGCCGGAGCTCCGATATGGAGACCGATAAGgtacttccgt ... taatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaggagatttgctttactgcattaaatatctatttctttttataatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG
                               tctatttctttttat  CT-rich tract
               tttactgcattaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgattgatattgtatcaataaaaatctgacattcgaatactgtattaggagatttgctttactgcattaaatatctatttctttttataatttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - gacattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta