Sequence
atgc intronic sequence ATGC exonic sequencegtaaacttttggaaactcctggcctacatcaaaagtaatattactatgttgatgctattttgtttatcagGTAAACAGTGAGCATCCGTTAGCAAAGGCCATTGTCGAGTACGCGAAGAAATTCAGAGACGACGAAGAGAACCCTGCCTGGCCAGAAGCCTGTGATTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63440.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------gtaaacttttggaaactcctggcctacatcaaaagtaatattactatgttgatgctattt-tgtttatcagGTAAACAGTGAGCATCCGTTAGCAAAGGCCATTGTCGAGTACGCGAAGAAATTCAGAGACGACGAAGAGAACCCTGCCTGGCCAGAAGCCTGTGATTTTG
| ||||| || | | ||| | | | | |||| | | | |||| | ||| || ||||| ||||||||||| || | || ||||||||||| ||||| || |||||||||||||| || |||||||| || | ||||||||||| ||||| |
aaatgtttaattaaaacattaagcttgtgaaccatgctttttacaaattc--gcccataaagtttgaatatttacaacataggtgctctgaatgtgtaccagGTGAACAGTGAGCACCCACTGGCTAAGGCCATTGTGGAGTATGCTAAGAAATTCAGAGAAGATGAAGAGAATCCCACTTGGCCAGAAGCAAAGGATTTCG
upper sequence: AT1G63440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 4
---------------------gtaaacttttggaaactcctggcctaca-------tcaaaagtaatatt-actatgttgatgctattt-tgtttatcagGTAAACAGTGAGCATCCGTTAGCAAAGGCCATTGTCGAGTACGCGAAGAAATTCAGAGACGACGAAGAGAACCCTGCCTGGCCAGAAGCCTGTGATTTTG
|| ||| | | | | | | || | | ||| ||| || | |||| |||| | | ||| |||||||| ||||||||||| || ||||| ||||||||||| ||||| || |||||||||||||| |||| ||||| ||| ||||||| ||||| | |||||||
gccaaatatcatttttaagctgtccactcaagcagtaactttgtcaaccatgatgttgagaaggaatgtttaaaatgtagatgttctggatgtgtatcagGTGAACAGTGAGCACCCATTAGCCAAGGCCATTGTTGAGTATGCCAAGAAATTCAGAGAAGACGGAGAGAGCCCCACCTGGCCTGAAGCAAGAGATTTTG
upper sequence: AT1G63440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03640.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gtaaacttttggaa---actcctg------gcctacatcaaaagtaatattactatgttgatgctattt-tgtttatcagGTAAACAGTGAGCATCCGTTAGCAAAGGCCATTGTCGAGTACGCGAAGAAATTCAGAGACGACGAAGAGAACCCTGCCTGGCCAGAAGCCTGTGATTTTG
|||| |||||| | || || ||| || || | | ||| |||| | | || | ||| || ||||| ||||||||||| || |||| ||||||||||| || || || |||||||||||||| || |||||||| || |||||||||||||| ||||| |
tcaaacagtccattcaagaagtaagcttttgaaccatgcttttgcaaatcgcccacgaagaatgaatacttagaatgtaggtactctggatgtgtaccagGTGAACAGTGAGCACCCACTAGCCAAGGCCATTGTAGAATATGCTAAGAAATTCAGAGAAGATGAAGAGAATCCCACCTGGCCAGAAGCCAAAGATTTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcctggcctacatcaaaagtaatattactatgttgatgctattttgtttatcagGTAAACAGTGAGCATCCGTTAGCAAAGGCCATTGTCGAGTACGCGAAGAAATTCAGAGACGACGAAGAGAACCCTGCCTGGCCAGAAGCCTGTGATTTTG
tgttgat putative branch site (score: 4)
ttttgttt putative PPT
aaaagtaatattacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacttttggaaactcctggcctacatcaaaagtaatattactatgttgatgctattttgtttatcagGTAAACAGTGAGCATCCGTTAGCAAAGGCCATTGTCGAGTACGCGAAGAAATTCAGAGACGACGAAGAGAACCCTGCCTGGCCAGAAGCCTGTGATTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC