Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcacactatccttaccttattttttctctgaacagttttagtttttttagagatagtccgtttatctgagataaacattcatttgtatagagtatctgtgactgtacttaacccataattatgtgtttagGTATCCGTTGTTGCTCCAAACACACCGGCCATGTATGAGATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65890.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G33110.1 (Glycine max), 3'ss of exon 1
gtatgtcacactatccttaccttattttttctctgaacagttttagtttttttagagatagtccgtttat-ctgagata---aacattcatttgtatagagtatctgtgactgtacttaacccataattatgtgtttagGTATCCGTTGTTGCTCCAAACACACCGGCCATGTATGAGATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
| || || | ||| | || | ||| || || || | || || | | || | | |||||| | | || || | | ||||| ||||||| || | || || |||| || || |||||||||||||| ||||| || ||||||||||| ||||| || ||| | |||||||||||||| || |
-----------------------------------agcatttctcttttatatacacatatatgattcatgctaaagtactcaaagattaattatctggagtatacat-atactaattttctggt--ttatgcaac-agGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcatttgtatagagtatctgtgactgtacttaacccataattatgtgtttagGTATCCGTTGTTGCTCCAAACACACCGGCCATGTATGAGATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
acttaac putative branch site (score: 3)
ataattatgtgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcacactatccttaccttattttttctctgaacagttttagtttttttagagatagtccgtttatctgagataaacattcatttgtatagagtatctgtgactgtacttaacccataattatgtgtttagGTATCCGTTGTTGCTCCAAACACACCGGCCATGTATGAGATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT