Sequence
atgc intronic sequence ATGC exonic sequencegtgtgcttgaaatgtggaagaaaacttaacagctcactgtttgttgatttgcattttgaacactgattatgttctatttcttcttatttttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05190.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 8
----------gtgtg---cttgaaatgtggaagaaaactt-aacagctcactgtttgttgatttgcattttgaacactgattatgttctatttcttcttatttttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC
|| || ||| |||| | | ||| | | || | || || || | || || |||| | | | | | |||||||||| ||||| || ||||| ||||| |||||||| || |||||||||||||| | || || ||||||||||| ||||||||||| ||||||||
gtaattaattgtatgacacttaaaattcttctgtatgctttgatataacaaagctt-cagagttatacagattctcatggtttgaaattattaccctgtgatct-atcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 8
gtgtgcttgaa-atgtggaag--aaaacttaacagctcactgtttgttgatttgcattttgaa----cactgatt---atgttcta----tttcttcttatt-tttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC
||| || | | || | |||| | | | ||||| | || || | || |||| ||| | | | | | | | | | | |||||||||| ||||| || ||||| ||||| |||||||| || |||||||||||||| | || || ||||||||||| ||||||||||| ||||||||
--gtgattaattgtatgacacttaaaagtctgctgtatgctgttgatagagcaaagcttcagagttatacagattctcatggtttgaaattattaccctgtgatctatcagGTTTCTGTGTTTGATTCAGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTGTATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 9
gtgtgcttgaaatgtggaagaaaacttaacagctcactgtttgttgatttgcattttgaacactgattatgttctatttcttcttatttttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC-
| | |||||||||| ||||| || ||||| ||||| |||||||| || ||||| || ||||| | || || ||||||||||| ||||||||||||||||||||
-----------------------------------------------------------------------------------------gtatcaggtttctgtgtttgattcagttgtccaaggaggtgactcagtttgggagGGTCTTCGAGTGTATAATGGAAAGATATTTAAGCTTGAGGAACATCTAGACAG
upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S180_110V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------gtgtgcttgaaatgtggaagaaaacttaacagctcactgtttgttgatttgc-attttgaacactgattatgttctatttcttcttatttttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC
| | | || | || | |||| | | | || ||| | |||| | | || |||| || || | | | |||||||||| ||||| ||| |||| ||||| || || || |||||||||||||||||||| ||||| || | |||||||| ||||| ||||||||
gttagtgatgacaattctattgctccctttcgaaataactcaggaactttagtaaggtctctattttatattcaggtgtaagtatgtttaagcacttggttgagaagttttgaatgacgagttgtttttagtagtgcttatcagacatcattttct---tggatcagGTTTCTGTATTTGATTCGATTGTGCAAGGAGGAGATGGAGTGTGGGAAGGACTTCGGATTTATAAGGGTAAAGTGTTCAAGCTAGAGGAGCATCTAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgatttgcattttgaacactgattatgttctatttcttcttatttttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC
cactgat putative branch site (score: 3)
tgttctatttcttctt putative PPT
tatttcttcttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgcttgaaatgtggaagaaaacttaacagctcactgtttgttgatttgcattttgaacactgattatgttctatttcttcttatttttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT