Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttcagaaatgtgaattgcctaaagatcctacacttcattcacaaggaacaatgttctttcttttttttgcagGTTCCTCTGTTTGCTAATATGGATGAGAGATTACTAGACGCAATATGTGAGAGACTAAAGCCAAGTCTATACACAGAGAGCACTTACATAGTGCGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G23460.1 (Glycine max), 3'ss of exon 6
gtaagttttcagaaatgtgaat--tgcctaaagatcctacacttcattcacaaggaacaatgttctttcttttttttgcagGTTCCTCTGTTTGCTAATATGGATGAGAGATTACTAGACGCAATATGTGAGAGACTAAAGCCAAGTCTATACACAGAGAGCACTTACATAGTGCGAGAAG
|| ||| | | | ||| | || | |||| ||||||| | || | || | | | ||||||||||| ||||| || |||||||| | || || || || ||||||||| |||| ||||| ||| |||| |||||| | |||||||||||| | ||||
gtgagtatactggcctgttctttatgacatgagatatatgtcttcatttgttc---ataagtcttttgtatactcatccagGTTCCTCTCTTTGCCAACATGGATGAACGTTTGCTTGATGCTATATGTGAGCGACTGAAGCCTAGTTTATATACAGAGGGAACTTACATAGTGAGGGAAG
upper sequence: AT1G19780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G02560.1 (Glycine max), 3'ss of exon 6
gtaagttttcagaaatgtgaattgcctaaagatcctacacttcattcacaaggaacaatgttctttcttttttttgcagGTTCCTCTGTTTGCTAATATGGATGAGAGATTACTAGACGCAATATGTGAGAGACTAAAGCCAAGTCTATACACAGAGAGCACTTACATAGTGCGAGAAG
|| ||| | | | ||| || | | | || | || | |||| | | | || | ||||||||||| ||||| || |||||||| | || || || || ||||||||| || | ||||| ||| |||| |||||| |||||||||||||| | ||||
gtgagtatactggcctgttcttta--tgagatttatataagtcttcattttttcacaagtcttgtgtatattcattcagGTTCCTCTCTTTGCCAACATGGATGAACGTTTGCTTGATGCTATATGTGAGCGATTGAAGCCTAGTTTATATACAGAGGGCACTTACATAGTGAGGGAAG
upper sequence: AT1G19780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0018g00410.t01 (Vitis vinifera), 3'ss of exon 6
gtaagttttcagaaatgtgaattgcctaaagatcctacacttcattc-acaaggaacaatgttctttcttttttttgca-gGTTCCTCTGTTTGCTAATATGGATGAGAGATTACTAGACGCAATATGTGAGAGACTAAAGCCAAGTCTATACACAGAGAGCACTTACATAGTGCGAGAAG
||| || || | | || || ||||| ||| | |||| || | || || | || | | | |||| ||||||||||||||| ||||||||||| ||||| || || || || |||||||| || | || ||| ||| ||| || | |||||||||||||| ||||
gtacgtagtctatactttggat-gcctatggattcattccttcctttgataaaaaatcttattagtatatacatatgcaagGTTCCTCTGTTTGCAAATATGGATGAAAGATTGCTTGATGCCATTTGTGAGAGGCTGCAACCGAGTTTATTCACGGAAAAAACTTACATAGTGCGGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctaaagatcctacacttcattcacaaggaacaatgttctttcttttttttgcagGTTCCTCTGTTTGCTAATATGGATGAGAGATTACTAGACGCAATATGTGAGAGACTAAAGCCAAGTCTATACACAGAGAGCACTTACATAGTGCGAGAAG
gcctaaa putative branch site (score: 3)
tgttctttcttttttt putative PPT
ttctttctttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttcagaaatgtgaattgcctaaagatcctacacttcattcacaaggaacaatgttctttcttttttttgcagGTTCCTCTGTTTGCTAATATGGATGAGAGATTACTAGACGCAATATGTGAGAGACTAAAGCCAAGTCTATACACAGAGAGCACTTACATAGTGCGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA