Sequence
atgc intronic sequence ATGC exonic sequencegtatatttcctattatagagtgtgtagtgcttttcccttaccgaggctttgtatgttgttaatgacatggtgtcttctttttttccaacttgaagATGATGGCGGTGGAATGGATCCCGATGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACGACGATTGGACAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36270.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G05800.1 (Glycine max), 3'ss of exon 5
gtatatttc---ctattatagagtgt-gtagtgcttttcccttaccgaggctttgtatgttgttaat---gacatggtgtcttctttttttccaacttgaagATGATGGCGGTGGAATGGATCCCGATGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACGACGATTGGACAGT
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atatattttagactaatttttactgttatagtaattcttttggtttgatattcaagttattggcaacaaaggcttactggagcacgtgtttcctg--tgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACGATTGGACAGT
upper sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 3
gtatattt---cctattatagagtgt-gtagtgcttttcccttaccgaggctttgtatgttgttaat---gacatggtgtcttctttttttccaacttgaagATGATGGCGGTGGAATGGATCCCGATGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACGACGATTGGACAGT
||||||| |||| | | | ||| |||| |||| || | | ||| || | | | || | ||||| || ||||||||| ||||||||| | || ||| | |||||||||||||||| || || |||||||||||||| || || || ||||||||||
atatattttagcctaatctttactgttatagtaatttttttggtttgatattcaagttattggcaacaaaggcttattggagcacatgtttcctg--tgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
upper sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g02740.t01 (Vitis vinifera), 3'ss of exon 4
gtatatttcctattatagagtgtgtagtgcttttcccttaccgaggctttgtatgttgttaatgacatggtgtcttctttttttccaacttgaagATGATGGCGGTGGAATGGATCCCGATGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACGACGATTGGACAGT
| | ||||| || || | ||| | ||| | | ||||| | | | | || | | | ||||||||| |||||||||||||| || | | |||||||||||||| || ||||| ||||||||||| || || || |||||||| |
----gtatggtattaatatatgaccagatgtggcttcttgcatcattttt-----taataaatgataagtgggcaactatggatgttttgtacagATGATGGAGGTGGAATGGATCCTGAATCTATTCGGAAATGCATGAGCTTGGGTTACTCTTCAAAGAAGTCGAACACAACAATTGGACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgaggctttgtatgttgttaatgacatggtgtcttctttttttccaacttgaagATGATGGCGGTGGAATGGATCCCGATGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACGACGATTGGACAGT
tgttaat putative branch site (score: 3)
tgtcttctttttttcc putative PPT
ttcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatttcctattatagagtgtgtagtgcttttcccttaccgaggctttgtatgttgttaatgacatggtgtcttctttttttccaacttgaagATGATGGCGGTGGAATGGATCCCGATGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACGACGATTGGACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT