Sequence
atgc intronic sequence ATGC exonic sequence...catatttagcctatagcttttttgggtctttgcttctcttacggagttctatcatgtctttttcttttctaatctgataccattgttttataacttacagGGAAATCGCCCAAGGGTTAATGAAATATCAACCAGATATCATAATCAGTGTTCATCCGTTGATGCAACATGTCCCACTTCGTGTCCTAAGATCAAAAGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g25580.1 (Oryza sativa), 3'ss of exon 2
-------catatttagcctatagcttttttg-ggtctttgcttctcttacggagttctatcatgtctttttcttttctaatctgataccattgttttataacttacagGGAAATCGCCCAAGGGTTAATGAAATATCAACCAGATATCATAATCAGTGTTCATCCGTTGATGCAACATGTCCCACTTCGTGTCCTAAGATCAAAAGGC
| | ||||| || || |||| |||| | | || || | || | | | | || || || | || |||| | | ||| || | || |||| | |||||||| ||||||||| | || |||||||| ||||| || ||||| ||||||||||| || ||||||| ||||||||
gatggagtgagtatgtgctatactttagctgtggtccttgcctatatttgtgaataacatggtatataata----tcgaaattgcctctcttatttt----cctgcagAGAGGTTGCAAAAGGTCTCATGAAATACCAACCAGATGTAATTATCAGTGTCCATCCTTTAATGCAGCATGTCCCACTCCGAATCCTAAGGTCAAAAGGT
upper sequence: AT4G31780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G12120.1 (Glycine max), 3'ss of exon 2
---catatttagcctatagcttttttgggtctttgcttctcttacggagttctatcatgtctttttcttttctaatctgataccattgttttataacttacagGGAAATCGCCCAAGGGTTAATGAAATATCAACCAGATATCATAATCAGTGTTCATCCGTTGATGCAACATGTCCCACTTCGTGTCCTAAGATCAAAAGGC
||| || | |||| ||| | | | |||||| | | | || | | | | | || | | | || ||| |||||| || | ||| |||| ||||||||||||| |||||||| ||||||||||| ||||| ||||||| || || |||||||| | |||| ||||| ||
ttccatggttcagaaaatactttcttgtgcatgcgtatctcttctcaaatacaat-gtaacatcacatgtcatagtt--aaaatatcttttctctttttacagCGAGGTTGCCAAAGGCCTAATGAAATATCAGCCAGATATAATAATCAGTGTGCATCCACTGATGCAGCACGTTCCACTTCGAATTTTAAGGTCAAAGGGT
upper sequence: AT4G31780.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G33780.1 (Glycine max), 3'ss of exon 2
-catattt-agcctatagcttttttgggtctttgcttctcttacggagttctatcatgtctttttcttttctaatctgataccattgttttataacttacagGGAAATCGCCCAAGGGTTAATGAAATATCAACCAGATATCATAATCAGTGTTCATCCGTTGATGCAACATGTCCCACTTCGTGTCCTAAGATCAAAAGGC
||| ||| || | |||| ||| | | || |||||| | | || | | | | ||| | || | | | |||||| || | || |||| ||||||||||||| |||||||| ||||||||||| ||||| ||||||| || || |||||||| | | || || || ||
ccatgtttcagaaaaatactttcttgtgcatgtgtatctcttctcaaatatgatgtaacatcaaatgtcacagttaaaatatctttttctctt--tttacagCGAGGTTGCTAAAGGCCTAATGAAATATCAGCCAGATATAATAATCAGTGTGCATCCACTGATGCAGCACGTTCCACTTCGAATTTTGAGGTCTAAGGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctatcatgtctttttcttttctaatctgataccattgttttataacttacagGGAAATCGCCCAAGGGTTAATGAAATATCAACCAGATATCATAATCAGTGTTCATCCGTTGATGCAACATGTCCCACTTCGTGTCCTAAGATCAAAAGGC
ttataac putative branch site (score: 2)
attgttttataactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catatttagcctatagcttttttgggtctttgcttctcttacggagttctatcatgtctttttcttttctaatctgataccattgttttataacttacagGGAAATCGCCCAAGGGTTAATGAAATATCAACCAGATATCATAATCAGTGTTCATCCGTTGATGCAACATGTCCCACTTCGTGTCCTAAGATCAAAAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - tttttgg
- - - - - - - - - - - - - - - - cttctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatacca