Sequence
atgc intronic sequence ATGC exonic sequencegttggttctctcactcatccattgtttattttcctggctttagttacatgattcagacgcattatcaccgttcaatccgttatggtttactctgatattgtggaccttgaatcctagGTCAGCAGCACAACCAATTGATGATGACGATAATGTAGAATTAGATAAGAGCAATGTTCTCTTGATGGGGCCTACTGGCTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G33360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 2
-----------------------gttggttctctcactcatccattgtttattttcctggctttagttacatga----ttcagacgcattatcaccgttca---atccgttatg----gtttactctgatattgtggaccttgaatcctagGTCAGCAGCAC-----AACCAATTGATGATGACGATAATGTAGAATTAGATAAGAGCAATGTTCTCTTGATGGGGCCTACTGGCTCTG
|||| | ||| || | | || | | || | || ||| || || || || | | | |||| | ||||| | || || | | | || | | | | | | | | ||||||||||||| ||| ||| |||| || ||||||||||| || |||||||||||||||||
gtcagtttctttctaccaccttagttgttcttcttgttcttggaatgatgaagctcgtctattcttgcacaagaacaattaggatcgatgaatatctttcagtgactaattatgtggtatataagctaaaacaattagGTCTGGAGCAGATTTGGGTGGTTTTGATGGAGAAGCTGATGATGACGATGGTGTTGAACTAGAGAAAAGCAATGTTCTATTAATGGGGCCTACTGGCTCA-
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G28260.1 (Glycine max), 3'ss of exon 3
gttggttctctcactcatccattgtttattttcctggcttt---agttaca--tgattcagacgcattatcaccgttcaatccgtta--tggtttactctgatatt--gtggaccttgaatcctagGTCAGCAGCACAACCAATTGATGATGACGATAATGTAGAATTAGATAAGAGCAATGTTCTCTTGATGGGGCCTACTGGCTCTG
|| || | ||||| || | | | | | | | ||| | ||||||| | | || | | |||| | | ||| | || || || | | ||| || || | | ||||||||||||||||| ||| |||| ||||| ||||||||||||||||| || || || || |
--------cacggtaaatatatggggtatttacccaagtgtcaaaatcatagtttgttctttcacattatctatttgctatgattgaattggtggatttcaatactagGTCAGCCGCAGATTCAGG---AGCTTCAGAAGTATTAGATGATGACGATAATGTGGAACTAGAAAAGAGTAATGTTCTCTTGATGGGTCCAACAGGGTCAG
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 3
gttggttctctcactcatccattgtttattt-tcctggctttagttacatgattcagacgcattatcaccgttcaatccgttatggtttactctgatattgtggaccttgaatc-----ctagGTCAGCAG---CACAACCAATTGATGATGACGATAATGTAGAATTAGATAAGAGCAATGTTCTCTTGATGGGGCCTACTGGCTCTG
| || || | |||| || | | | ||| || | | || || | | | | |||| || | || | | | | | || | |||| || || || | | ||||||||||||||||| || |||| || || ||||||||||||||||| || || || || |
--------catggtaaatatatggggaatttacccaagtgtcaaaatcatagtttggtct--ttcacattatcta-tttgctatgattgaatcggtggatttcaatactagGTCAGCCGCAGATTCAGGAGTTTCAGAAGTATTAGATGATGACGATAATGTGGAGCTAGAGAAAAGTAATGTTCTCTTGATGGGTCCAACAGGGTCAG
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------gttggttctctcact--catccattgtttattttcctggctttagttacatgattcagacgcattatcaccgttcaatccgttat-----ggtttactctgatattgtggaccttgaatcctagGTCAGCAGCACAACCAATT---------GATGATGACGATAATGTAGAATTAGATAAGAGCAATGTTCTCTTGATGGGGCCTACTGGCTCTG
| |||||| | | | || | | | | | | || | | | || ||| | || || | || | | || | ||||| | |||| | ||||||||| |||| || || | | |||||| ||| ||| || | || ||||||||||||||||||||||| || |||||||| |
gttagttcttaatgggatttctttcatcttattttttttacctcactatcatataagaaggctctgtgctaatatttctcttgttactaaaaaagaaatacatatgtaacaattgggaaattttgttgtaaccttttcaagctgcaggtttttgttccttggataaaactaaacttgtgcat-ttgactactagGTCAGGAGCAGAATCAGGTACATCAGAGGTTGATGATGATTCTGTGGAGCTGGAAAAGAGCAATGTTCTCTTGATGGGTCCAACTGGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcaccgttcaatccgttatggtttactctgatattgtggaccttgaatcctagGTCAGCAGCACAACCAATTGATGATGACGATAATGTAGAATTAGATAAGAGCAATGTTCTCTTGATGGGGCCTACTGGCTCTG
ctctgat putative branch site (score: 4)
tgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttctctcactcatccattgtttattttcctggctttagttacatgattcagacgcattatcaccgttcaatccgttatggtttactctgatattgtggaccttgaatcctagGTCAGCAGCACAACCAATTGATGATGACGATAATGTAGAATTAGATAAGAGCAATGTTCTCTTGATGGGGCCTACTGGCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA