Sequence
atgc intronic sequence ATGC exonic sequence...tgaaatcctttgttccacaactttatttgttgacatgcttgcctcatatttgtctaaaaactgtagcccccaaactaaaaatctgaattttggcgtttagGTGTGCTGTTCTGGTCATGGGAAGAATGGTGCTTTATGTGTTCTTCGGCAGTCAATTAGACCGGAAATGATTACTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51660.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 12
tgaaatcctttgttccacaac--tttatttgttgacatgcttgcctcatatttgtctaaaaactgtagcccccaaactaaaaatctgaattttggcgtttagGTGTGCTGTTCTGGTCATGGGAAGAATGGTGCTTTATGTGTTCTTCGGCAGTCAATTAGACCGGAAATGATTACTGAG
| || | ||||| || ||| ||| ||| || | | ||| || | | || | | || | | | | | | |||||||||||||||||||||| ||||||||| || | |||||||| ||||| |||||| | || ||| |||||||||||
ttaatattaatattccataatggtttgtttac-attatgtttatcattgttctgtttacattcaatattttttgtttcacatatattgagct-gccatgcagGTGTGCTGTTCTGGTCATGGAAAGAATGGTTCTCTGTGTGTTCTGCGGCAATCAATTCGCCCAGAAGTGATTACTGAG
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------------------------------tgaaatcctttgttccacaactttatttgttgacatgcttgcctc-ata----tttgtctaaaaactgtagcccccaaactaaaaatctgaattttggcgtttagGTGTGCTGTTCTGGTCATGGGAAGAATGGTGCTTTATGTGTTCTTCGGCAGTCAATTAGACCGGAAATGATTACTGAG
|||| || |||| | || ||| | || | || || ||| | ||| || | | || | | || | | | | | ||||||||||||||||||||||| || |||||| || | |||||| | ||||| |||||| | || ||| |||||||||||
gtcagtatttcttttttttccttggtgttttaatctgagcactattaccttacttggatagggaaaccaggtggggggagtgaatgaag-ccgttgtactacctgcttaaatattattactattatttccataatggtctgtttacattcaatattttttgtttcacatatattgagct-gctatgtagGTGTGCTGTTCTGGTCATGGAAAAAATGGTTCTCTTTGTGTTTTGCGGCAATCAATTCGCCCAGAAGTGATTACTGAG
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 12
tgaaatcctttgttccacaactttatttgttgacatg-cttgcctcatatttgtctaaaaactgtagcccccaaactaaaaatctgaattttggcgtttagGTGTGCTGTTCTGGTCATGGGAAGAATGGTGCTTTATGTGTTCTTCGGCAGTCAATTAGACCGGAAATGATTACTGAG
|| | | ||||| | || || | | || |||||| || | ||| | | | | | | | | | || ||||||| |||||||||||||| |||||||||||| | || |||| | ||| |||||| | || |||||||| || |||
tgcatctaccttttccaaatctaagaaccttagagtatcctgtctcatagtt-tgaaaatatgtttgttattattattattttttttggggtacttttcagGTGTGTTGTTCTGGTCATGGAAAGAATGGTGCTCTCTGCATTCTGCAGCAATCAATTCGTCCAGAAATGATCACGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttgtctaaaaactgtagcccccaaactaaaaatctgaattttggcgtttagGTGTGCTGTTCTGGTCATGGGAAGAATGGTGCTTTATGTGTTCTTCGGCAGTCAATTAGACCGGAAATGATTACTGAG
aactaaa putative branch site (score: 2)
taaaaatctgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaatcctttgttccacaactttatttgttgacatgcttgcctcatatttgtctaaaaactgtagcccccaaactaaaaatctgaattttggcgtttagGTGTGCTGTTCTGGTCATGGGAAGAATGGTGCTTTATGTGTTCTTCGGCAGTCAATTAGACCGGAAATGATTACTGAG
tgaaatc
- - - - - - - ccacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaatc