Sequence
atgc intronic sequence ATGC exonic sequence...taagattgaagttgtttctgttattataatgattgcttggctaattcagagtttgatatattcattccattaatttattgttgcaacacttctttctcagGTAATAGAGTTTCAGCAAAGGAAATGCTGTGTCATATTTGATCTTTCATGTAATCTTACAAGGATTCTAGAGTTCTGTACTCATGAGATTCCTCAAGCAT
Basic information
species | Glycine max |
transcript | GLYMA04G39780.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39780.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G22010.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------taagattgaa--gttgtttctgttattataatgattgcttggctaattcagagtttgatatattcattccattaatttattgttg---caacacttctttct-cagGTAATAGAGTTTCAGCAAAGGAAATGCTGTGTCATATTTGATCTTTCATGTAATCTTACAAGGATTCTAGAGTTCTGTACTCATGAGATTCCTCAAGCAT
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gtcagattataagcttggatcattttcatcgattaagttttcgtagtaattgaatagttttccctgaatgattgtggttcttattctg-catttcccttacaagtttttgtagtactctatttgcttctttgtccggtttttgattcgtcttgtctttatgcagGTAATGGAGTTTCAGCAAAGGAAATGTTGTGTGATATTTGAGCTTTCAAGCAATCTCGCAAGGGTCTTAGAATTCTGCACTTACGCAATGCCACAAGCAT
upper sequence: GLYMA04G39780.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g01490.t01 (Vitis vinifera), 3'ss of exon 8
taagattgaagttgtttctgttattataa--tgattgcttggctaattcagagtttgatatattcattccattaattta-ttgttgcaacacttctttctcagGTAATAGAGTTTCAGCAAAGGAAATGCTGTGTCATATTTGATCTTTCATGTAATCTTACAAGGATTCTAGAGTTCTGTACTCATGAGATTCCTCAAGCAT
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---gtccggactagtccaggttttccccccttccttgccccatcctttttcctttccccttttctacatcttgggtgtaattattttaaaacatactgtgcagGTTTTGGAGTTTCAGCAACGGAAATGCAGTGTAATATTTGACCTCTCATGTAATCTTGCGAGGGTATTGGAGTTCTGTACCCGTGAGATACCTCAAGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagagtttgatatattcattccattaatttattgttgcaacacttctttctcagGTAATAGAGTTTCAGCAAAGGAAATGCTGTGTCATATTTGATCTTTCATGTAATCTTACAAGGATTCTAGAGTTCTGTACTCATGAGATTCCTCAAGCAT
cattaat putative branch site (score: 3)
cacttctttctc putative PPT
tttgatatattcattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taagattgaagttgtttctgttattataatgattgcttggctaattcagagtttgatatattcattccattaatttattgttgcaacacttctttctcagGTAATAGAGTTTCAGCAAAGGAAATGCTGTGTCATATTTGATCTTTCATGTAATCTTACAAGGATTCTAGAGTTCTGTACTCATGAGATTCCTCAAGCAT
- - - - - - -gtttctg
- - - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - gagtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca