Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtatctctaagacctaaccctattgttttagcagatgctagttatagagagactaatgatttaggtgtaattagGTGGTCGCAAATAGCTAAATTCTTACCGGGAAGAACAGACAATGAGATAAAGAACTATTGGCACTCTCATTTGAAAAAGAAATGGCTCAAGTCTCAGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G25560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 2
-----------------------gtaagtgtatctctaagacctaa--ccctattgttttagcagatgctagttatagagagactaatgatttaggtgtaattagGTGGTCGCAAATAGCTAAATTCTTACCGGGAAGAACAGACAATGAGATAAAGAACTATTGGCACTCTCATTTGAAAAAGAAATGGCTCAAGTCTCAGAGC
|||| | | | ||| | | | ||||| | || | | ||| ||| ||| ||| | | ||||||||| || ||| | | || || ||||| |||||||||||||| || ||||||||||| || |||||||||||| | | ||| || ||
cagaaattcaacactactttccagtaaaataaaatttgcagtgtaatttcttcctcttttaattaagactgctga--gagcaact--tgaattatat-tggctagGTGGTCACAGATATCACAGCATTTGCCAGGAAGGACAGACAATGAGATTAAAAACTATTGGCATTCATATTTGAAAAAGAGAGTGGCCAAAGCTAAGGAA
upper sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 2
--------------gtaagtgtatctctaagacctaac-cctattgttttagcagatgctagtta----tagagagactaa--tgatttaggtgtaattagGTGGTCGCAAATAGCTAAATTCTTACCGGGAAGAACAGACAATGAGATAAAGAACTATTGGCACTCTCATTTGAAAAAGAAATGGCTCAAGTCTCAGAGC
|| | | | | | | ||||| ||| | | || ||| | |||| || ||| ||| | | ||||||||| | ||| | | || || ||||| |||||||||||||| || ||||||||||| || |||||||||||| | | ||| || ||
actttccggtaaaataaaatattgcagtgtaatttctttcctataatttcttccacttttaattaagactgctgagagcaacttgaattatat-tggctagGTGGTCACGGATATCACAGCATTTGCCTGGAAGGACAGACAATGAGATTAAAAACTATTGGCATTCATATTTGAAAAAGAGAGTGGCCAAAGCTAAGGAA
upper sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G31280.1 (Glycine max), 3'ss of exon 2
-----gtaagtgtat-ctctaagacctaaccctattgttttagcaga-------tgctagttatagagagact----aatgatttaggtgtaatt----agGTGGTCGCAAATAGCTAAATTCTTACCGGGAAGAACAGACAATGAGATAAAGAACTATTGGCACTCTCATTTGAAAAAGAAATGGCTCAAGTCTCAGAGC
|||||| |||| || | |||||| ||| | | | || | || || | || | ||| | ||| |||||||| |||||||| | || || ||||| || |||||||||||||| || |||||||| || |||||||||||||| | |||| | ||
cattttccagtgtacactctttgatttt-tcctatttctttgctataatattttttttattaatggaaaattctgaaaacaaattaaatcatattggccagGTGGTCTCAAATAGCACAGCATTTGCCAGGAAGGACTGACAATGAGATAAAAAATTATTGGCATTCATATTTGAAAAAGAAAGAGATCAAAGCCAAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattgttttagcagatgctagttatagagagactaatgatttaggtgtaattagGTGGTCGCAAATAGCTAAATTCTTACCGGGAAGAACAGACAATGAGATAAAGAACTATTGGCACTCTCATTTGAAAAAGAAATGGCTCAAGTCTCAGAGC
gactaat putative branch site (score: 2)
taatgattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtatctctaagacctaaccctattgttttagcagatgctagttatagagagactaatgatttaggtgtaattagGTGGTCGCAAATAGCTAAATTCTTACCGGGAAGAACAGACAATGAGATAAAGAACTATTGGCACTCTCATTTGAAAAAGAAATGGCTCAAGTCTCAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA