Sequence
atgc intronic sequence ATGC exonic sequence...gcaattatgtgtctcagaaaaaatatttaccttttagaatgttgttgatgtttgccatttagtgatctatctatctaaaagcactgatgtattcatgtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGAAGGTCCTCACTTTATATTCCCTGGAGGTG
Basic information
species | Glycine max |
transcript | GLYMA03G01870.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G01870.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G076841_T01 (Zea mays), 3'ss of exon 1
gcaattatgtgtctcagaaa-aaatatttaccttttagaatgttgttgatgtttgccatttagtgatctatctatctaaaagcactgatg-tattcatgtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGAAGGTCCTCACTTTATATTCCCTGGAGGTG
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--aaatgggtatttctgtttcatgtgtttatcctagtacacagattaaattttcatctgttcgattgatatttattgttcatggttattgctctcctttcagATCTGGCATGACAACATGCCTTATGGTAAGATTGCTGAAAGAAAAGGTCATCAAGGGTGGATGAAGCATGAAGGTTCGTACTTCATTTTTCCTGGCGGTG
upper sequence: GLYMA03G01870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------gca-attatgtgtctcagaaaaaatatttaccttttagaat-gttgttgatgttt----------------------gccatttagtgatctat---ctatctaaaagcactgatgtattcatgtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGAAGGTCCTCACTTTATATTCCCTGGAGGTG
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gtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgatgtctagttttgcatggttagaaacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
upper sequence: GLYMA03G01870.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 1
gcaattatgtgtctcagaaaaaatatttaccttttagaatgttgttgatgtt--tgccatttagtgatctatctatctaaaa-gcactgatgtattcat-gtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGAAGGTCCTCACTTTATATTCCCTGGAGGTG
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----ccttgttttaatatattgctttttaaccatcaaaaaatgctttctttcaatgccataaattattacaactacttgaagtatatgtctatctcctttgcagATCTGGCACAGCAACATGCCACACAATAAAATTGCTGACAGGAAAGGTCACCAGGGATGGATGAAAGAAGAAGGCATGTACTTCATTTTCCCTGGGGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgtttgccatttagtgatctatctatctaaaagcactgatgtattcatgtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGAAGGTCCTCACTTTATATTCCCTGGAGGTG
cactgat putative branch site (score: 3)
tatctaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaattatgtgtctcagaaaaaatatttaccttttagaatgttgttgatgtttgccatttagtgatctatctatctaaaagcactgatgtattcatgtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGAAGGTCCTCACTTTATATTCCCTGGAGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - gtgtctc
- - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg