Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaattgtatgatattctggaaaataaaagtgataaccagttttcttaatctgaggtgatatttatttataaccacagTCTCAACCGGTGGAGGTTAATGTCGTGAGCCATCCTGTCCAGAGGTTTGCAGTTTGGTTTGGAGGCTCTGTGCTTTCATCAACTCCTGAGTTTTTCGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13180.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 7
-----gtaagaaaattgt---atgatattctggaaaataaaagtgata---accagttttcttaatctgaggtgatatttatttataa-------ccacagTCTCAACCGGTGGAGGTTAATGTCGTGAGCCATCCTGTCCAGAGGTTTGCAGTTTGGTTTGGAGGCTCTGTGCTTTCATCAACTCCTGAGTTTTTCGCG
| | |||| || | || ||||| | | || || | || || ||| | || || |||||| | ||||| || || |||||||| ||||| | ||| |||| ||||||| |||||||||||||||||||| || |||||| ||||||| ||||| ||||| ||
tagtgatgtgttggttgttagttggttttatggaagggcagactgctatatatttattgctttggcctggcatt-tacttttttatatttggagtctgcagTCGCAGCCAGTGGAGGTAAATGTACTCAGCAATCCAATCCAGAGATTTGCAGTTTGGTTTGGAGGATCAGTGCTTGCATCAACACCTGAATTTTTTACG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 7
gtaagaaaattgtatgatattctggaaaataaaagtgataaccagttttcttaatctgaggtgatatttattt-------------------ataaccacagTCTCAACCGGTGGAGGTTAATGTCGTGAGCCATCCTGTCCAGAGGTTTGCAGTTTGGTTTGGAGGCTCTGTGCTTTCATCAACTCCTGAGTTTTTCGCG
| | ||| || |||||| | | | || || || ||| || | || | ||||| || | | |||||| || || |||||||| ||||| | |||||||| |||| || |||||||||||||||||||| || || ||| ||||||| ||||| ||||| ||
-ttgtcaccttg-atatagttctggcaggttgtactgctatacatatttattgctttggtcttgcatttacttcttctacttcattaatttggtgcctacagTCACAGCCAGTGGAGGTAAATGTACTCAGCCATCCAATCCAAAGATTTGCAGTTTGGTTTGGAGGATCAGTACTTGCATCAACACCTGAATTTTTTACG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 7
------gtaagaaaattgt--atgatattctggaaaataaaagtgata---accagttttcttaatctgaggtgatattt-----atttataacc-acagTCTCAACCGGTGGAGGTTAATGTCGTGAGCCATCCTGTCCAGAGGTTTGCAGTTTGGTTTGGAGGCTCTGTGCTTTCATCAACTCCTGAGTTTTTCGCG
| | |||| || |||| ||||| | | || || | || || ||| | ||| |||| |||| |||||| || || |||||||| ||||| | ||| |||| ||||||| | |||||||||||||||||| || |||||| | ||||| ||||| ||||| ||
ttagtgatgtgttggttgttaattgtattttggaaggtctgactgctatatatttattgctttggcctggcatttacttttttatatttggaacctacagTCGCAGCCAGTGGAGGTAAATGTACTCAGCAATCCAATCCAGAGATATGCAGTTTGGTTTGGAGGATCAGTGCTTGCGTCAACACCTGATTTTTTTACG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaaaattg----------tatgatattctggaaaataaaagtgataaccagtt-ttcttaatctgaggtgat-------atttattt-ataaccacagTCTCAACCGGTGGAGGTTAATGTCGTGAGCCATCCTGTCCAGAGGTTTGCAGTTTGGTTTGGAGGCTCTGTGCTTTCATCAACTCCTGAGTTTTTCGCG
||||| | ||| || || |||| | ||| || | ||| || | || | | | |||| ||| || ||||| ||||| ||||| || ||||| || ||||||||| ||||||||| ||| |||||||||||||||||||| ||| ||||||| || || ||||| |||
gtaagtattttgggttttatcccattatgttctttagaatgtaatataactttggttattaatgatataaaaaggctgaccggatttgttttgcccccccagTCACAACCAGTGGAAGTCAATGTAGTCAGCCATCCTATCCAGAGGTATGCGGTTTGGTTTGGAGGCTCTGTACTTGCATCAACACCCGAATTTTTTGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaagtgataaccagttttcttaatctgaggtgatatttatttataaccacagTCTCAACCGGTGGAGGTTAATGTCGTGAGCCATCCTGTCCAGAGGTTTGCAGTTTGGTTTGGAGGCTCTGTGCTTTCATCAACTCCTGAGTTTTTCGCG
ttataac putative branch site (score: 2)
tgatatttatttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaattgtatgatattctggaaaataaaagtgataaccagttttcttaatctgaggtgatatttatttataaccacagTCTCAACCGGTGGAGGTTAATGTCGTGAGCCATCCTGTCCAGAGGTTTGCAGTTTGGTTTGGAGGCTCTGTGCTTTCATCAACTCCTGAGTTTTTCGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG