Sequence
atgc intronic sequence ATGC exonic sequencegtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
Basic information
species | Glycine max |
transcript | GLYMA13G42430.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G13890.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgc-agGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
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------------------------------------------------------------------------------gtttcttgaattatctatactaataag---aagtctttgtatttaggttttaatttctttgtggttttgcttgtgtttaattagGTTTGCAGAGATGTGGAAAGAGTTGTAGATTAAGATGGATAAATTATCTAAGACCTGATCTTAAACGTGGAAGCTTCTCTCCTCAAGAAGCTGCTCTTAT
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 1
gtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
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-----------------gcacttatacacatatacatgggttttgtttcttgaattatctatactaat------aagaagtctttgtatttaggttttaatttc-----------tttgtggttttgct-----tgtgtttaatta--------------gGTTTGCAGAGATGTGGAAAGAGTTGTAGATTAAGATGGATAAATTATCTAAGACCTGATCTTAAACGTGGAAGCTTCTCTCCTCAAGAAGCTGCTCTTAT
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
gtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
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--------------------------------------------------ctctttctctctctctctctaatcact---tttgcaggctaaccccacaatattt-tcatggctttct-----ctttgttttcttctggttaaat-cttgatggtg-gcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
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--------------------------------------cagaaagttttcttgattgccaat------cagtttactatttttatacatt--------gaatttaaaaaaactaatgtct-atttcgtcgatcacaca--caattgctgta------acagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
aacttcttaattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC