Sequence
atgc intronic sequence ATGC exonic sequencegtgacatattcttttctctgcacttttaataacaatatatcccaattatatccatcacttctcgttgcatcaccacctaaaacctggctttccggttgttgacaaaacagAAGGAACGCTTGATTGGGATGCGCGGTTGAAGATTGCACTTGGAGCAGCGAGAGGACTGGCTTATCTCCATGAAGATTCAAATCCCCGAGTAATCCACCG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20300.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20300.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 3
-------gtgacatattcttttctctgcacttttaataacaatatatcccaattatatccatcacttctcgttgcat-caccacctaaaacctggctttccggttgttgacaaaacagAAGGAACGCTTGATTGGGATGCGCGGTTGAAGATTGCACTTGGAGCAGCGAGAGGACTGGCTTATCTCCATGAAGATTCAAATCCCCGAGTAATCCACCG
| | | | || |||| | | | ||| | | || | | | | | | | || ||| | | ||| || | || |||||| | | ||| | || || |||||||| ||| |||||||||| ||||| ||||| |||||| |||||||||| ||||||||||| |||||
catagcattaatggaattcattttctg-gttctatcttacatcaaaa--gaaatggagctttggttgaatatcttgtacattacccatgtcttggtattttagGTGCTGACAAGGGAAAGGGACCTCTCGACTGGGATGCACGGATGAAGATTGCCCTTGGTGCAGCAAGAGGATTGGCTTATCTTCATGAAGATTCTAATCC---------------
upper sequence: AT2G20300.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 6
-gtgacatattcttttctctgcacttttaataacaatatatcccaattatatccatcacttctcgttgcatcaccacctaaa-acctggct---ttccggttgttgacaaaacagAAGGAACGCTTGATTGGGATGCGCGGTTGAAGATTGCACTTGGAGCAGCGAGAGGACTGGCTTATCTCCATGAAGATTCAAATCCCCGAGTAATCCACCG
|| ||| | | || || || | | | | || || | | || || | | | ||| ||| | || || | | | | || ||| | | | ||| ||||||| || | |||| |||||||| ||||||||||||||||| ||||| || || || ||||| |||||
gctgccatctcatcttagttggttccttcctgatattggattccgcaattcatgaacaattgaaaaagtttgctaatttaattaccggactaatttgcagGTATAGATAAATTCAATGCTCCACTTAATTGGGAGGCTAGACTGAAAATTGCACTAGGAGCAGCGAGAGGACTAGCTTACCTTCACGAGGATTCGAATCC--------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacttctcgttgcatcaccacctaaaacctggctttccggttgttgacaaaacagAAGGAACGCTTGATTGGGATGCGCGGTTGAAGATTGCACTTGGAGCAGCGAGAGGACTGGCTTATCTCCATGAAGATTCAAATCCCCGAGTAATCCACCG
tgttgac putative branch site (score: 3)
taaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacatattcttttctctgcacttttaataacaatatatcccaattatatccatcacttctcgttgcatcaccacctaaaacctggctttccggttgttgacaaaacagAAGGAACGCTTGATTGGGATGCGCGGTTGAAGATTGCACTTGGAGCAGCGAGAGGACTGGCTTATCTCCATGAAGATTCAAATCCCCGAGTAATCCACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA