Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaacttcttctcattcactatcctgtaaaaatattagaagattaaaatgacaatatgtttctgttcagtgtcatgttaaagtatttgaatgattcactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
Basic information
species | Glycine max |
transcript | GLYMA05G30530.1 |
intron # | 6 |
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 6
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------gtatgtaa-cttcttctcattcactatcctg--taaaaatattagaagattaaaatgacaata-tgtttctgttcagtgtcatgttaaagtatttgaatgattcactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
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gtataatgttaccttctataaaaactttgacagatgtgcttgtttacttaaatatatcatgttactgaacttccactaatctatctgtttata--catgtatgatgatgcgttctatttcct--tggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgtaacttcttctcattcactatcctgtaaaaatattagaagattaaaatgacaatatgtttctgttcagtgtcatgttaaagtatttgaatgattcactgttcattgatcttc---cagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
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---------------------------------gtatagtatgctagtttgctgtccatatcatattactgaacttc-cattgat-caattatatgattctatttcttgggttcctcggttagGTCATTCCATTTGACAATAAAGGACAGCTCAAGGAAGCCTTTAACATAAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtaacttcttctcattcactatcctgtaaaaatattagaagattaaaatgacaata-tgtttctgttcagtgtcatgttaaagtatttgaatgattcactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
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-----------gtgcttgtttact------taaatatatcatgttactgaacttccactaatctatctgtttata--catgtatgatgatgcgttctatttcct--tggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttcagtgtcatgttaaagtatttgaatgattcactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
cattgat putative branch site (score: 4)
tcttcc CT-rich tract
ttaaagtatttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaacttcttctcattcactatcctgtaaaaatattagaagattaaaatgacaatatgtttctgttcagtgtcatgttaaagtatttgaatgattcactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA