Sequence
atgc intronic sequence ATGC exonic sequence...ggttagatgtatagatagggatcttttttacttcattaacccaagtggccctgaacaatggctcttaattgatatgcatgtgttatattttactgaacagGCTTTGGACTCCAATAGATGGTGAATTTGATGACTACATCATTAATCCGAAGCCTAGTGGCTATCAG
Basic information
species | Glycine max |
transcript | GLYMA01G43940.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43940.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g47120.1 (Oryza sativa), 3'ss of exon 10
---ggttaga-tgtatagatagggatcttttttacttcattaacccaagtggccctgaacaatggctcttaattgatatgcatgtgttatattttactgaacagGCTTTGGACTCCAATAGATGGTGAATTTGATGACTACATCATTAATCCGAAGCCTAGTGGCTATCAG
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tgagtctagaatttgctgaatagcacttgttccaatcaagaacttttagctatatctgattataaccttt----gcaaactgtctgctttatccatatatgcagGCTATGGACTCCAATTGATGGGGAGTTTGATGACTACATTATCAACCCTAAGGGTAGTGGTTACCAA
upper sequence: GLYMA01G43940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G106931_T01 (Zea mays), 3'ss of exon 10
ggttagatgtatagatagggatcttttttacttcattaacccaagt---ggccctgaacaatggctcttaattgatatgcatgtgttatattttac-tgaacagGCTTTGGACTCCAATAGATGGTGAATTTGATGACTACATCATTAATCCGAAGCCTAGTGGCTATCAG
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----attttccgagtccacaattcactacacaacagttatttcagtttaaaactttgttacttactcacttccaaactttgtaaattgtctgctccacctgcagGCTATGGACTCCAATTGATGGGGAGTTTGATGACTACATTATCAATCCTAAGGGTAGCGGTTACCAA
upper sequence: GLYMA01G43940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g02260.t01 (Vitis vinifera), 3'ss of exon 11
-ggttagatgtatagatagggatcttttttacttcattaacccaagtggccctgaacaatggctcttaattgatatgcatgtgttatattttactgaacagGCTTTGGACTCCAATAGATGGTGAATTTGATGACTACATCATTAATCCGAAGCCTAGTGGCTATCAG
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tggcatgatatgattactataatcagtccaaatgcattgcatccgtacctgctgcacttctg-tgaaaataatggctcatgtctcctttctcttgatgcagGCTTTGGACCCCCATTGATGGTGAATTTGATGATTACATTGTCAATCCAAAGCCTAGTGGCTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggccctgaacaatggctcttaattgatatgcatgtgttatattttactgaacagGCTTTGGACTCCAATAGATGGTGAATTTGATGACTACATCATTAATCCGAAGCCTAGTGGCTATCAG
ttttact CT-rich tract
atgtgttatatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggttagatgtatagatagggatcttttttacttcattaacccaagtggccctgaacaatggctcttaattgatatgcatgtgttatattttactgaacagGCTTTGGACTCCAATAGATGGTGAATTTGATGACTACATCATTAATCCGAAGCCTAGTGGCTATCAG
- - - - - - - - - - - - - - - cttcatt
- - - - - - - - - - - - - - - - - - -aacccaa
- - - - - - - - - - - - - - - - - - - - - - - - ccctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgt