Sequence
atgc intronic sequence ATGC exonic sequencegttaatatcttttgtctttcaggtttatgttttgtgttgtagatttatttctcacttatgaaaacaccaacactctctcctatttcagAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05190.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA07G30580.1 (Glycine max), 3'ss of exon 13
gttaatatcttttgtctttcaggtttatgttttgt-gttgtagatttatttctcacttatgaaaacacca-acactctctcctatttc--agAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
|| || |||| || | || || |||||| |||| ||| | | || | | | |||| |||||| ||| |||||||| ||||| |||||||| || ||||| |||||||| ||||||||||| |||| |||||||| |||||||| || |||||||||||||| |
gtacatg-ctttcgtaatacattagcatattttgttattgttcttttttcctcctgacattatttcttgatgcacttctctctattttgtagAAAACTGAACAACAAGTGCAAGGTGTGCTAAACCTGATTGATCTGGCTGGAAGTGAAAGACTGTCAAGGAGTGGGGCAACTGGGGACCGGTTAAAGGAAA
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA08G06690.1 (Glycine max), 3'ss of exon 15
gttaatatcttttgtctttcaggtttatgttttgt-gttgtagatttatttctcacttatgaaaacacca-acactctctcctatttc--agAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
|| || ||||||| |||| || |||||| ||| ||| | | || | | | |||| | | |||||| |||| |||||| | ||||| |||||||| | ||||| |||||||| ||||||||||| |||| |||||||| |||||||| || |||||||||||||| |
gtacatg-cttttgtaattcattagcatattttgttactgttcttttgtcctccggacattatttcctgatgcacttttttctattttgtagAGAACTGAAAAACAAGTGCAAGGTGTGTTAAACCTGATTGATCTGGCTGGAAGTGAAAGACTGTCAAGGAGTGGGGCAACTGGGGACCGGTTAAAGGAAA
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G32450.1 (Glycine max), 3'ss of exon 13
gttaatatcttttgtctttcaggtttatgttttgtgttgtagatttatttctcacttatgaaaacaccaacactctctcctatttcagAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
|| | ||||| || | || ||| ||| |||| | ||||| | || | || | | || ||| |||||| || ||||| |||||||| | ||||| |||||| | ||||||||||| |||| || ||||| ||||||||||| |||||||| ||||| |
-gtactgactttt-tcatacattggtatatttactgttct---tttatcttgacaccatttcctgatgtacttttctctcgtttatagAACACTGACCAACAAGTGCAAGGTGTGTTAAACCTGATTGATTTGGCTGGAAGTGAAAGACTGTCCAGGAGTGGGGCAACCGGGGACCGGTTGAAGGAAA
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G06880.1 (Glycine max), 3'ss of exon 14
--gttaatatcttttgtctttcaggtttatgttttgtgttgtagatttatttctcacttatgaaaacaccaacactctctcctattt-cagAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
| | || ||| | | ||| ||| | ||| | | || | || || | || | |||| | | ||| |||||| || ||||| |||||||| | ||||| |||||| | ||||||||||| |||| || ||||| || |||||||| |||||||| ||||| |
gtactga-atttttcatacatt-ggtatatttactgtttcttttatcttgacaccatttcctgatgtact-----tttctcttgctcatagAACACTGACCAACAAGTGCAAGGTGTGTTAAACCTGATTGATTTGGCTGGAAGTGAAAGACTGTCGAGGAGTGGAGCAACCGGGGACCGGTTGAAGGAAA
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 14
gttaatatcttttgtctttcaggtttatgttttgtgttg-tagatttatttct-cacttatgaaaac--accaaca-ctctctcctatttc-----------agAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
|| || | || | | ||| ||| | | || || || || | ||| | || || | | ||| || | | | || |||| || ||||| |||||||||||||| | ||||| ||||||||||| |||||||||||||| || | ||| | |||| ||||||||||| ||||| |
gtacattcccttgcaatactacatttttgtactcttctgctacatacatgcgtgcacaaacaaacactcatccacatctgttgaccactttgttgatctgctagAGTACCGAACAACAAGTACAAGGTGTCTTAAACCTCATTGATCTTGCGGGAAGTGAGCGACTCTCCAAGAGTATGTCAACTGGAGACCGGTTGAAGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttgtagatttatttctcacttatgaaaacaccaacactctctcctatttcagAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
ttctcac putative branch site (score: 2)
cactctctcctatttc putative PPT
tagatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatatcttttgtctttcaggtttatgttttgtgttgtagatttatttctcacttatgaaaacaccaacactctctcctatttcagAGCACTGAACAGCAAGTACAAGGTGTTCTTAACCTAATTGATCTTGCTGGAAGTGAGCGACTTTCAAGGAGCGGGGCAACCGGAGACCGGTTAAAGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA