Sequence
atgc intronic sequence ATGC exonic sequencegtacctttcttcatgcttcctgtttttgtgttttattatcatcctcttttcttttgtgttcagaaatgacctaacaggtaacttctattttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35610.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g38930.1 (Oryza sativa), 3'ss of exon 2
gtacctttcttcatgcttc--ctgtttttgtgttttattatcatcctcttttcttttgtgttcagaaatgacctaacaggtaacttctattttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG
| | || || || |||| | | | || || || || | ||| ||| | |||| | | ||| || | || | || ||| |||||||| || || |||||||||||||||| |||||||| || ||||||||||||||||| | ||||| || || || | || || | |||
actttgtgcatcttgtttatactgtccctttcgtctaaaattctctgtaattttcttgggttgtttat--acctgaaatgtatttttttcttgagttgccagGGCATGTATCAGCAGCTTCGGCTAGAACCATATGCTGTGCATACTACTTTCCAGTATGCAGGTACTGTGGGAAAGCGTCATAGATTGCGTGAAGCAATGC
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------gtacctttcttcatgcttc-ctgtttttgtg--ttttattatcatcctcttttctt----------ttgtgttcagaaatgacctaacaggtaacttctattttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG
|| || | || || |||| ||| | || | ||| | | | ||||||||| | ||||| | |||| ||| ||| ||||||||||||| |||||||| | || |||||||| ||||| |||||||| || |||||||| || |||||||| |||||| | || ||||| | ||||
gtaggatctagttaacaattacaaattccttcttttctgattttatataatatctactattctactttctgttttcttttacacaattaactgtccaagtgaatcttgcgtggaccctgtgatgtagagaaacaaactgtgttcagttttt-cctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 6
gtacctttcttcatgcttcctgtttttgtgtttt-attatcatcctcttttcttttgtgttcagaaatgacctaacaggtaacttctatt--ttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG
|| | ||| ||| |||||| | || | | || | | | ||| | ||| | | | ||| || | ||||||||||||||||| || || |||||||| |||||||| |||||||||||||| ||||| || ||||| || || || ||||| || | || ||
---tctgccatcaaacttgagaattttgtacctagatccatgacatagaacacattaaactttgcattgaacatctttctaagccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttcttttgtgttcagaaatgacctaacaggtaacttctattttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG
cttctattttc CT-rich tract
ttctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctttcttcatgcttcctgtttttgtgttttattatcatcctcttttcttttgtgttcagaaatgacctaacaggtaacttctattttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG