Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G25800.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 6
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
|| || | ||||||||| | | | | | | | || | || | || | | || | ||||||||||| ||||| |||||||||||||||||||| || || ||||||||||| || |||||| |||| || |||| ||| | || ||| || |
--------------gtaagttctaca-attgttgttaataggttgtaattaatgtagtttaattgatgatca-aatacctcttttttcttttagATTCTTGGCAGTGGAATGTCAAATAAGATGTGGGAAAGCCTTGTTGAGCATGCAAAGACTTGTGTCTTAAGTGGAAAGCACTATGTATATTATGCTATTG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtct-agATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
|| | | || | || ||| || | || || | | | | || | | |||| |||| ||||||||||| ||||| ||||||||||||||| | || || || |||||||| || |||||| |||| || || ||| || || ||| | || |
------------------gtaagattatttcctattcagcatttttcttcttttttt-cttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 6
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
|| ||| | | |||| | | || | | || | || || || || | | || | | | |||||||| |||||||||| ||| ||||||||||||||||||||| || || |||||||| || |||||||| | || || || | ||||| || || | |
gtaagt-cttattattcctctttgtaacttatattaaga--attttgtttctttaaaactaaaatttggttttcttcttctgatattt--tcagATTCTTGGCAGTAACATGTCAAATAAGATGTGGGAAAGTCTTGTTGAGCATGCGAAGACATGTGTTTTGAGTGGCAAACACTATATATATTACTCAAGCG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 6
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
|| | |||| | | | | | || | || | || || || | | | || | ||| | ||| | |||||||| || ||||| |||||||||||||||||||| || || ||||||||||| ||||||||| |||| || |||| |||| | |||||| || ||
----gtaagttctatgatacct-gtttttgcttactatattgtga--tttatggtattccctatatggtttgacagcccttgttctttttatagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGAGCATGCAAAGACATGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtc-tagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
||| || || | || | || || || | | | || | ||| | ||| | |||||||| || ||||| |||||||||||||||||||| || || || |||||||| || |||||| |||| || |||| |||| | |||||| || ||
-------------------gtaagttctatgataccttattgtga--tttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaa---cattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
|| || | | |||| || || |||| || | || ||| || | ||| || | || | ||| |||| || ||||||||||||||||||||||||||||| || | ||||||||||| || || | | || || ||| | ||| | || ||| |||| |
--------------gtaagtgcaatatttagttgctgaattagaaatacaatgatctaat-cttgtttcctgatatatttttctggttgctgt--agATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
| | || | | | || | | | || | || ||| | | | ||||||||||||||||||||||||||||||||||||| |||||||||||| ||||| || ||||| ||||| ||||| ||| |||| ||| | || |
---------------------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggt-ctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 5
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
||| | || | || | ||| || | | || | ||| || ||| | | | ||||||||||||||||||||||||||||||||||||| |||||||||||| ||||| || ||||| ||||| ||||| ||| |||| ||| | || |
-------------------gtaag-taatgagtttttttctctctctttctctctctttctttcagc--tcatg--tagttggt-ctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
atttgat putative branch site (score: 5)
tttgtct CT-rich tract
atgagtaattatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG