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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttattatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG

Basic information

species Glycine max
transcript GLYMA20G28950.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 3
----------------------------------cttttcctgcttaacagtagttggg---gctcatgtga-------tccagatataactggacaacttattatgttctttctgacattatttcgttgccaaaat-------------ttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
                                   || |   | ||| ||||  ||  |   | |  |||||       |||   |  | ||   |    ||   | | |  |   |||    |  |   |  ||||                 |||||||||||||| ||||| || || || || || ||||| |||||||||||||||||||| ||||| |||
gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG

upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 3
----------------------------------------cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttat-tatgttctttctgac--attattt------cgttgccaaaatt------------tggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
                                        | |||| ||  |  ||   |||     |  | | |  ||||| |  |  ||  | |||  ||||   |  |      || | ||      |||  | ||||||            |  |||||||| ||||| ||||| || || ||||| ||||||||||| ||||| || |||||||| ||||| |||
gtaatataagccacatacctgcattgtattattcttgcttcctttcttgagtttcaa-ggttatatgttgttttagtcagatgtgtcaagagcagttacatatgcattagccagttgatcacttgatctacgtgtctaaaattgtgtctattgtctatcagGATCGTATTATTGCTCGGCTGCAACAGCCTTATTCCCTTGACTGCATACCAGTTGAAGCTGAATACCAG

upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 3
-cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttattat-gttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
 | ||  || || |  |    ||  | ||    |       |   || | |  | | | |  | |   ||| | |||| ||||   ||     || |  ||||||||||| || ||||| || || || || ||||| || ||||||||||| ||||||||||||||||||
acattagcttctgagtacgtcttaagactgccttatcttttagtcaatttgtgaccctctagttgaagtttattacatcatttgtctgttt--atataacagGATCGCATCATTGCTCGTCTCCAACAACCTTATTCGCTAGATTGCATTCCAGTTGAAGCAGAATATCAG

upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 3
cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttat--tatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
 |||       ||     |  ||   ||   |  |  ||| || ||    |  | | ||  | |||    | |         || |||    | ||||||||||||||||||||||||| || || || || ||||| || ||||||||||| || |||||||||| ||||
-tttcttcatatacatacacatgcatcttcagc-acacaggtaaaatgacatcattaatcctgtgtaacatatatgcgggaatctttgttccattttggcagGATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG

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|208024965|gb|GD822411.1|GD822411
EST:     AAGATGTTATTCAGAACAAG                         GATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCT
genomic: AAGATGTTATTCAGAACAAGgtaatgtaat ... aatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCT
EST: gi|192296888|gb|FG990249.1|FG990249
EST:     AGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGAACAAG                         GATCGCATTATAGCTCGCCT
genomic: AGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGAACAAGgtaatgtaat ... aatttggcagGATCGCATTATAGCTCGCCT
EST: gi|192322441|gb|FK014922.1|FK014922
EST:     AGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGAACAAG                         GATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCT
genomic: AGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGAACAAGgtaatgtaat ... aatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggacaacttattatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
                      ttctgac  putative branch site (score: 2)
          ttattatgttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttattatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC