Sequence
atgc intronic sequence ATGC exonic sequencegttcttcctctattccatttcacaggctacttgttttaatcatttttatttggatatgcattttttttggactttgttgtcttctgttttcgacggaaacctctctttgcagCCTATGTTGGATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGTCCTCAT
Basic information
species | Glycine max |
transcript | GLYMA05G30530.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 2
gttcttcctctattccatttcacaggctacttgttttaatcatttttatttggatatgcattttttttggactttgttgtcttctgttttcgacggaaacctct------ctttgcagCCTATGTTGGATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGTCCTCAT
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----------------------------------gttagtcatttctacaagtgtcagcgtagtgcctatctgccatt-tcttcggcataataccataacattttgattgcctatcagCCGATGCTTGATGTGCCTATATATGGAAGAATTGCAACGATTGAGCTCTTCCGGCCTCAT
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 2
--------gttcttcctctattccattt-cacaggctacttgttttaatcatttttatttggatat-----gcattttttttggactttgttgtcttct--------gttttcgacggaaacctctct-ttgcagCCTATGTTGGATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGTCCTCAT
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gtacatacatctctattctgtcaagcttatatggattaagttccatgtacattagagtataaagttcaaaaactttgttgtcatgctttgttttgttagtaatataagaatctgctggatgttcctatattgcagCCTATGTTGGACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCAT
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 2
gttcttcctctattccatttcacaggctacttgttttaatcatttttatttggatatgcattttttttggactttgttgtc----ttctgttttcgacggaaacctctctttgcagCCTATGTTGGATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGTCCTCAT
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----------------gataaaaagtagagttcatttcattgttaaaatcagaacttttttattccaaaagcatgattgcaaaggtcaagttgacagaaaattattttatttgcagCCTATGTTGGATGTGCCAATATATGGGAGAATAGCAACACTTGAGCTTTTTCGCCCCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcattttttttggactttgttgtcttctgttttcgacggaaacctctctttgcagCCTATGTTGGATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGTCCTCAT
cctctctttgc CT-rich tract
tttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttcctctattccatttcacaggctacttgttttaatcatttttatttggatatgcattttttttggactttgttgtcttctgttttcgacggaaacctctctttgcagCCTATGTTGGATGTGCCGATATATGGAAGAATTGCAACACTTGAACTCTTCCGTCCTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA