Sequence
atgc intronic sequence ATGC exonic sequence...acatgttccattatatatccttaataaatagaaaatgtatcgtgaaatggataacctgtctaaattggattattgatcaattaattaaaactactatcagGTGGATTACATTCTTGGAGACAACCCTAGAGCAACAAGTTACATGGTCGGATACGGAGAGAACTATCCACGACAAGTTCATCATCGTGGTTCGTCTATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------acatgttccattatatatccttaataaatagaa-aatgtatcgtgaaatggataac----ctgtctaaattggattatt--gatc-aattaattaaaact----actatcagGTGGATTACATTCTTGGAGACAACCCTAGAGCAACAAGTTACATGGTCGGATACGGAGAGAACTATCCACGACAAGTTCATCATCGTGGTTCGTCTATTG
| | | |||||| | | | ||||| || || | || || | | | |||| | || | |||| || || || | | | ||||||||| ||| ||||||| |||||||| ||||| || ||||||||||| || || ||| |||| |||| | |||||||| | ||||| || ||||
gtactgaaaaattgtctctatttttaagttttagttcatataagagaaaatgggcacaattataaggaccaagtgaatagtttaacctactttcaattgaactttttcattctgtaaaatctatcagcaggatctaagtacttgacatgttaaatcttcagGTGGACTACCTTCTTGGGGACAACCCAAGAGCTACTAGTTACATGGTGGGCTATGGAAGCAACTTCCCACAAAGGGTTCATCACAGAGGTTCATCCATTG
upper sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------acatgttccattatatatccttaataaa--tagaaaatgtatcgtgaaatggataacctgtctaaatt--ggattattgatcaattaattaaaactactatcagGTGGATTACATTCTTGGAGACAACCCTAGAGCAACAAGTTACATGGTCGGATACGGAGAGAACTATCCACGACAAGTTCATCATCGTGGTTCGTCTATTG
| | ||||||||| | | | ||| || | || | | || | | || | || | ||| | ||| ||||||||||| ||||||||||||||||| ||||| || ||||||||||| || || ||| | |||||||| |||||||| || || || ||||| || ||||
gtaatttgatcctggactggattgtagaatgttatggatgagattatatatgagtgagggtgtttgaagatactctttcttgtgattggaataaacaagtacagagttttaaatgggatgatttgtaa-acttgcagGTGGATTATATTCTTGGAGACAACCCAAGAGCCACGAGTTACATGGTGGGGTATGGAAACAACTATCCTCGACAAGTCCACCACCGAGGTTCCTCGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatggataacctgtctaaattggattattgatcaattaattaaaactactatcagGTGGATTACATTCTTGGAGACAACCCTAGAGCAACAAGTTACATGGTCGGATACGGAGAGAACTATCCACGACAAGTTCATCATCGTGGTTCGTCTATTG
aattaat putative branch site (score: 3)
taaattggattattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatgttccattatatatccttaataaatagaaaatgtatcgtgaaatggataacctgtctaaattggattattgatcaattaattaaaactactatcagGTGGATTACATTCTTGGAGACAACCCTAGAGCAACAAGTTACATGGTCGGATACGGAGAGAACTATCCACGACAAGTTCATCATCGTGGTTCGTCTATTG
- - - - - - - - - - - aataaat
- - - - - - - - - - - - - - -agaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attaaaa