Sequence
atgc intronic sequence ATGC exonic sequence...cgatggaaattgtcatatagaaaaagaaaatgtagctaatccaatttcttaattaaattaagtttgatgaatgctaattagtcgttgaatacatatatagGAGTGAACAAGGACGGGACGGTGCGTCATTTCTTCCACCGACCGTCGAAGGCATACACGACGGGAACAAGAAAGCGACGTAAAGTCCACACTGATTCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28500.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 2
--cgatggaaattgt-----catatagaaaaagaaaatgtagctaatccaatttcttaat---taaattaa--gtttgatgaatgc-------taattagtcgttgaatacatatatagGAGTGAACAAGGACGGGACGGTGCGTCATTTCTTCCACCGACCGTCGAAGGCATACACGACGGGAACAAGAAAGCGACGTAAAGTCCACACTGATTCTGA
| || ||||| | | || || || | | | | || ||||| || | | || | ||| || || ||| || | || | || ||| |||| |||||||||| |||| | || ||||||||||| ||||||||||| ||||||||||| || || ||||| || || || |||| || |
gtgggtgtaaattcttttttcttacagtggaatcagaatcggtagcttaaaattcttgataaatgagttgatcgttgcgtgcatttgtgggtgtaaataaatttgaaaaattaattcagGTGTGAGCAAGGACGGGCTGGTGAGGCACTTCTTCCACCGGCCGTCGAAGGCGTACACGACGGGGACGAGGAAGCGGCGGAAGGTGCACAGCGACGAGGT
upper sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g48130.1 (Oryza sativa), 3'ss of exon 2
-----cgatggaaattgtcatatagaaaaagaaaatgtagctaatccaatttcttaattaaattaagtttgatgaatgctaattagtcgttgaatacatatatagGAGTGAACAAGGACGGGACGGTGCGTCATTTCTTCCACCGACCGTCGAAGGCATACACGACGGGAACAAGAAAGCGACGTAAAGTCCACACTGATTCTGA
| | | | | | | | || | | | | || | ||||| | || || | | || || | | |||||| ||||||||| | | || || ||||||||||| ||||||||||| ||||||||||| || | ||||| || || || ||||| || |
gattacatttgcatctcttaactcattcgtgagagcagtggcagtgtggcactcta-ccatattaaccgtactgttctctttct-gccgctgttaattt---cagGAGTCGGCAAGGACGGCCTGATCCGGCACTTCTTCCACCGCCCGTCGAAGGCGTACACGACGGGGACGCGGAAGCGGCGGAAGGTGCACACCGACGAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttaattaaattaagtttgatgaatgctaattagtcgttgaatacatatatagGAGTGAACAAGGACGGGACGGTGCGTCATTTCTTCCACCGACCGTCGAAGGCATACACGACGGGAACAAGAAAGCGACGTAAAGTCCACACTGATTCTGA
tgctaat putative branch site (score: 2)
aattaaattaagtttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgatggaaattgtcatatagaaaaagaaaatgtagctaatccaatttcttaattaaattaagtttgatgaatgctaattagtcgttgaatacatatatagGAGTGAACAAGGACGGGACGGTGCGTCATTTCTTCCACCGACCGTCGAAGGCATACACGACGGGAACAAGAAAGCGACGTAAAGTCCACACTGATTCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - -aatccaa
- - - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtttga