Sequence
atgc intronic sequence ATGC exonic sequence...gtgatgcgtacaatcttaggcaaggattagacacatgctatatccaggttgtttggtggtggatctgatatctcttatgtttgtgttttgattattttagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52660.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
gtgatgcgtacaatcttaggcaaggattagacacatgctatatccaggttg--tttggtggtggatct----gatatctcttatgtttgtgttttgattattt---tagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
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--------tacagtgtcaaattaagat-aatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
upper sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
gtgatgcgtacaatcttaggcaaggattagacacatg-ctatatccaggttgtttggtggtggatc-tgatatctcttatgtttgtgttttgatt--attttagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
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---atttaagctat-ttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
upper sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgatgcgtacaatcttaggcaaggattagacacatgcta---tatccaggttgtttggtggtggatctgatatctcttatgtttgtgttttgattattttagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
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-tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattg-acaagcaatctgctt-ttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggttgtttggtggtggatctgatatctcttatgtttgtgttttgattattttagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
ttttgat putative branch site (score: 4)
ttatttt CT-rich tract
tgttttgattatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgcgtacaatcttaggcaaggattagacacatgctatatccaggttgtttggtggtggatctgatatctcttatgtttgtgttttgattattttagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC