Sequence
atgc intronic sequence ATGC exonic sequencegtatccttgtccttctctcgtaaacattaactatgtatatatcggctagaccaatatatatgctgcttatggccgaattagtccatgttatgcattttgaagccatgtagttaaattgattggttgtgcatacatatatctatgttcagGCTTCCAAGCTTTCGAGATGATGGCGATCGCAGCTGTTGGAAACAACTTGATCACATACGTATTCAATGAGATGCATTTCCCTTTGTCAAAATCCGCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G33440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G33440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os11g12740.1 (Oryza sativa), 3'ss of exon 1
gtatccttgtccttctctcgtaaacattaactatgtatatatcggctagaccaatatatatgctgcttatggccgaattagtccatgttatgcattttgaagccatgtagttaaattgattggttgtgcatacatatatc-tatgttcagGCTTCCAAGCTTTCGAGATGATGGCGATCGCAGCTGTTGGAAACAACTTGATCACATACGTATTCAATGAGATGCATTTCCCTTTGTCAAAATCCGCAAA
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---------------gttcgt-----ttaattagttagttactctcttaatccat-tatttcttgggtagaaatatgttgcttgatctgatttgttcttgt-ttgtgtttgtgttttgttggatatcgtttgcattgatgatgattgcagGGATCCAGGCGTTCGAGATGATGGCGATCGCGGCGGTGGGGAACAACCTGATCACCTACGTCTTCAACGAGATGCACTACCCGCTGTCAAAGTCGGCCAA
upper sequence: AT1G33440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0089g01010.t01 (Vitis vinifera), 3'ss of exon 1
gtatccttgtccttctctcgtaaacattaactatgtatatatcggctagaccaatatatatgctgcttatggccgaattagtccatgttatgcattttgaagccatgtagttaaattgattggttgtgcatacatatatctatgttcagGCTTCCAAGCTTTCGAGATGATGGCGATCGCAGCTGTTGGAAACAACTTGATCACATACGTATTCAATGAGATGCATTTCCCTTTGTCAAAATCCGCAAA
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----------------------------------------gtgggtagtgctcattca---gttattttttttttaaataatatatat-acttgttttgagaatatata--tatattgattgattaatgtttggtgggtg---attcagGTCTTCAGGCATTTGAGATGATGGCTATTGCTGCAGTTGGGAACAATCTCATAACATATGTGTTCAATGATATGCACTTCCCTTTGTCAAAGTCAGCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgaagccatgtagttaaattgattggttgtgcatacatatatctatgttcagGCTTCCAAGCTTTCGAGATGATGGCGATCGCAGCTGTTGGAAACAACTTGATCACATACGTATTCAATGAGATGCATTTCCCTTTGTCAAAATCCGCAAA
aattgat putative branch site (score: 4)
tagttaaattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccttgtccttctctcgtaaacattaactatgtatatatcggctagaccaatatatatgctgcttatggccgaattagtccatgttatgcattttgaagccatgtagttaaattgattggttgtgcatacatatatctatgttcagGCTTCCAAGCTTTCGAGATGATGGCGATCGCAGCTGTTGGAAACAACTTGATCACATACGTATTCAATGAGATGCATTTCCCTTTGTCAAAATCCGCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG