Sequence
atgc intronic sequence ATGC exonic sequencegtattaacctgagagtcaatatctttatctaatctttacctgtctaaaaccgccaattgaatctgctgatgattcctatatctgttatctgttcaacagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35020.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 5
gtattaacctgagagtcaatatctttatctaatctttacctgtctaaaaccgccaattgaatctgctgatgattcctatatctgttatctgttcaacagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC---
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gtactgtcgccccag-cgctagctagattcagcattgagctcacctgttgtgt---ttgtggttactgactgttgcttctttgcacctccatcca---gAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTG---CAGAAGGGATGCACCATTTTGT
upper sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------------------------------------gtattaacctgagagtcaatatctttatctaatctttacctgtctaaaaccgccaattgaatctgctgatgattcctatatctgttatctgttca-acagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC
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gtaaacgcttgaattcaattgtggcttctatgctcaatgtgatgtgttggctctgctttaaacaattatgtaacttttccctttgtattctagcttgcgcatctatgaagatgggtggccagagtatgtagtccatcatggctgcaagatttttgtg--tcttatgacgcctttcggtctatgcagAATGTGAAAGCAGTTTTTGATGCTGCCATCAAGGTTGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAGAAAAAACAAAAG-AACTGTGTTATTCTCTGA
upper sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
-gtattaacctgagagtcaatatctttatctaatctttacctgtctaa-aaccgccaattgaatc-tgctgatgattcct-atat-ctgttatctgtt-caacagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC-----
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ggtcacaacgtg-----tcatagctctagcaattgtagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttcattgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACC------CAAGCAGAAGAAGAAGAAAAAAAAACAAAAGAACTGTGTCATACTCTGA
upper sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 6
-gtattaacctgagagtcaatatctttatctaatct-ttacctgtctaaaaccgccaattgaatctgctgatgattcctatat-ctgttatctgttcaacagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC-
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tttctgtaggtgggaacttgcaccaagattatgtcaactatgtagtgcactgtgtcaattatttttttgtttgatggcgatttattgtattctatt--gcagAATGTGAAAGCAGTTTTTGATGCCGCCATAAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAAGAAGCAAAAG-AACTGTGTCATTCTCTAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaaccgccaattgaatctgctgatgattcctatatctgttatctgttcaacagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC
tgctgat putative branch site (score: 3)
tctgttc putative PPT
aattgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaacctgagagtcaatatctttatctaatctttacctgtctaaaaccgccaattgaatctgctgatgattcctatatctgttatctgttcaacagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA