Sequence
atgc intronic sequence ATGC exonic sequencegtcaactcatttttcccataacatccattttcgtcggttttagctgaagctagttttgtctgttgacatttttaatttcaatgttagcatcaaactcatcattattgttcatattcgaatgcttcttatgtttgatggtggtaattaatgtgttgtgagcttgtaacttgctttgcagGGTCCTGAAGTTAGAAGTGGGGATGTAGCTCAACCTATTTTACTTAAAGAGGGACAAGAATTCTGTTTCACCACTATGAGAGGGGTTAGCACACATGACA
Basic information
species | Glycine max |
transcript | GLYMA01G40860.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 2
gtcaactcatttttcccataacatccattttcgtcggttttagctgaagctagttttgtctgttgacatttttaatttcaatgttagcatcaaactcatcattattgttcatattcgaatgcttcttatgtttgatggtggtaattaatgtgttgtgagcttgtaacttgctttgcagGGTCCTGAAGTTAGAAGTGGGGATGTAGCTCAACCTATTTTACTTAAAGAGGGACAAGAATTCTGTTTCACCACTATGAGAGGGGTTAGCACACATGACA
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---------------------------------------------------------------------------------------------gtatatctcagctgcatacatcaaaactaattctaca----acaacttaaattcttatgac-tgagtttgatggatgc-----agGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATCATGCTCAAGGAAGGTCAAGAGTTCAACTTCACGATTAAAAGAGGGGTGAGCACTGAAGACA
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G033526_T03 (Zea mays), 3'ss of exon 2
gtcaactcatttttcccataacatccattttcgtcggttttagctgaagctagttttgtctgttgacatttttaatttcaatgttagcatcaaactcatcattattgttcatattcgaatgcttcttatgtttgatggtggtaattaatgtgttgtgagcttgtaacttgctttgcagGGTCCTGAAGTTAGAAGTGGGGATGTAGCTCAACCTATTTTACTTAAAGAGGGACAAGAATTCTGTTTCACCACTATGAGAGGGGTTAGCACACATGACA
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---------------------------------------------------------------------------------------------gtatatctcagctgcatacatcaaaactaattctaca----acaacttaaattcttatgac-tgagtttgatggatgc-----agGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATCATGCTCAAGGAAGGTCAAGAGTTCAACTTCACGATTAAAAGAGGGGTGAGCAC--------
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 2
gtcaactcatttttcccataacatccattttcgtcggttttagctgaagctagttttgtctgttgacatttttaatttcaatgttagcatcaaactcatcattattgttcatattcgaatgcttcttatgtttgatggtggtaattaatgtgttgtgagcttgtaacttgctt--tgcagGGTCCTGAAGTTAGAAGTGGGGATGTAGCTCAACCTATTTTACTTAAAGAGGGACAAGAATTCTGTTTCACCACTATGAGAGGGGTTAGCACACATGACA
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--------------------------------------------------------------tcagtgagacagctctcactgct-gcaccaggccc-----cggtgaatatgttaaaacaaatgctata---------gcaacttaagttcttgtga--ctg-aatttgatggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAAGGGCAAGAGTTCAATTTCACAATTAAAAGAGGGGTGAGCACTGAAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttatgtttgatggtggtaattaatgtgttgtgagcttgtaacttgctttgcagGGTCCTGAAGTTAGAAGTGGGGATGTAGCTCAACCTATTTTACTTAAAGAGGGACAAGAATTCTGTTTCACCACTATGAGAGGGGTTAGCACACATGACA
ttgtaac putative branch site (score: 2)
cttgcttt CT-rich tract
taattaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaactcatttttcccataacatccattttcgtcggttttagctgaagctagttttgtctgttgacatttttaatttcaatgttagcatcaaactcatcattattgttcatattcgaatgcttcttatgtttgatggtggtaattaatgtgttgtgagcttgtaacttgctttgcagGGTCCTGAAGTTAGAAGTGGGGATGTAGCTCAACCTATTTTACTTAAAGAGGGACAAGAATTCTGTTTCACCACTATGAGAGGGGTTAGCACACATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG