Sequence
atgc intronic sequence ATGC exonic sequencegtgaagatctgtcacacttcattgtagttaatcacttccttgattaacgtgagccagttaagtatttacatgtcctctacatgatgcttttgataccagGTGAATTGGCACATGCATTGCGGTATCTAGCTTCTGTTGTCTCCCAAAGCTTTATGGCTTTTGGCGATATTCTTGAACTACACAAGAAGTTCCTGGAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39850.3 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39850.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G074241_T01 (Zea mays), 3'ss of exon 2
-------------gtgaagatc----tgtcacacttcattgtagt-taatcacttccttgattaacgtgagccagttaagtatttacatgtcctctaca-tgatgcttttg--ataccagGTGAATTGGCACATGCATTGCGGTATCTAGCTTCTGTTGTCTCCCAAAGCTTTATGGCTTTTGGCGATATTCTTGAACTACACAAGAAGTTCCTGGAGCT
|||| | | | | | | | | | || | | ||| ||| | | | | | | | | | ||| ||| | || |||| || ||||||||||| || ||| | || ||||| || || |||||||| || || ||||| ||||||||||| |||||||||||||||| || ||
gttggcattaatcttgaaagttccattattaaaaaaaaacaaaatcttggcagcgcttccatttctgtgcggtgttccttttggcatagagtttatgctctcatgttttcggaattacagGAGAGTTGGCACATGCTCTGAGGTTCTTGGCATCTGTGGTGTCACAAAGCTTCATAGCGTTTGGTGATATTCTTGAGTTACACAAGAAGTTCCTTGAACT
upper sequence: AT4G39850.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 20
gtgaagatctgtcacacttcattgtagttaatcacttccttgattaacgtgagccagttaagtatttacatgtcctctacatgatgcttttgataccagGTGAATTGGCACATGCATTGCGGTATCTAGCTTCTGTTGTCTCCCAAAGCTTTATGGCTTTTGGCGATATTCTTGAACTACACAAGAAGTTCCTGGAGCT
| ||| ||| ||| || | | | ||| ||| || | | | | | | | |||| | ||| | | || ||||||| |||||||||||||| ||| |||| |||||||| || ||||||||| | |||||||| |||||||| ||| | |||| ||||| | || ||
--gtagaattgttggact-----gttctcagttactctctttatcaccct---cttgccccccactgacatacgttgtac-tactatctta-----cagGTGAGCTGGCACATGCATTGAGGTTCTTAGCATCTGTTGTTTCTCAAAGCTTTTTAGCTTTTGGAGATATTCTAGAATTGCACAGAAAGTTTGTAGAACT
upper sequence: AT4G39850.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 20
gtgaagatctgtcacacttcattgtagttaatcacttccttgattaacgtgagccagttaagtatttacatgtcctctacatgatgcttttgataccagGTGAATTGGCACATGCATTGCGGTATCTAGCTTCTGTTGTCTCCCAAAGCTTTATGGCTTTTGGCGATATTCTTGAACTACACAAGAAGTTCCTGGAGCT
| || ||| ||| || | | | ||| ||| ||| | ||| | | |||| | || ||| | || ||||||| | |||||||||||| ||| |||| ||||| || || ||||||||| | ||||||||||| ||||||||| | |||| ||||| | |||||
--gtaggattgttggact-----gttctcagttactctctttatttcctcttgcccccca----ctgacatatgctgtac----tatctta-----cagGTGAGCTAGCACATGCATTGAGGTTCTTAGCATCTGTCGTTTCTCAAAGCTTTTTAGCTTTTGGCGACATTCTTGAATTGCACAGAAAGTTTGTAGAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacgtgagccagttaagtatttacatgtcctctacatgatgcttttgataccagGTGAATTGGCACATGCATTGCGGTATCTAGCTTCTGTTGTCTCCCAAAGCTTTATGGCTTTTGGCGATATTCTTGAACTACACAAGAAGTTCCTGGAGCT
ttttgat putative branch site (score: 4)
tgctttt CT-rich tract
ttaagtatttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagatctgtcacacttcattgtagttaatcacttccttgattaacgtgagccagttaagtatttacatgtcctctacatgatgcttttgataccagGTGAATTGGCACATGCATTGCGGTATCTAGCTTCTGTTGTCTCCCAAAGCTTTATGGCTTTTGGCGATATTCTTGAACTACACAAGAAGTTCCTGGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT