Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcattaggttctcatatcccaattattcactcttttttttttctctctctgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
Basic information
species | Glycine max |
transcript | GLYMA05G03380.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 3
--------gtaagttcattaggttctcatatcccaattattcactcttttttttttctctctc-tgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
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gcattgctgtgaaatg--tatgttgttttggca-ggcaatgcaccattaataatatgtatatcatgttgttctgatagtgtaacccaatcttaatgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTTCTGACAATAAGCTACCCTGGGCAAAG
upper sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 3
---------gtaagttcattaggttctcatatcccaattattcactcttttttttttctctctctgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
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ttttctgtgatgggcccattgtgatga-atatagctgtcatgttcaacttttaaagctgcatattgt--ctttgacaacgtaactcagttgttttctaaccagGAATTGGCTACAATGGCTTCCCTAGAGGTTGTTCCGATGACAAGCTTCCTTGGGCAAAG
upper sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------gtaagttcat-taggttctcatatcccaattattcactcttttttttttctctctctgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
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gtaagataatacgatcacacttgtgttttgatctctttgaacaacatgaagtgtggttgtatagtttatttcattttgtcacttagctggtacatgcgagacacatataaacgaggactcaaaaactt--tcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
upper sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g01370.t01 (Vitis vinifera), 3'ss of exon 3
---gtaagttcattaggttc--tcatatcccaattattcactcttttttttttctctctctgaaacgcaggtttcttactttgctttttcttct--gtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
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gatcatagttactgagcatcattcagattgtaat-gtgctttgagtttgatcgccgttatgatagttcttacaccatcattcggattctcttcttggtcagGCATTGGCTATAATGGGTTCCCAAGAGGCTGTTCAGATGACAAGCTCCCTTGGGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttttctctctctgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
ttcttac putative branch site (score: 2)
tttcttactttgcttt CT-rich tract
tttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcattaggttctcatatcccaattattcactcttttttttttctctctctgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG