Sequence
atgc intronic sequence ATGC exonic sequencegtaagactatgtcacctaagaatcaaattgttttagttactttatcaaatagaatcataggtattactattcatctttagttttatcatcttatagctaattcatgtttgttgaaatcttgcagGTTTTACAATTGACAAAGTTTGACTACAGACTAGCAAATGATCTAGATGAAGACATGCAAAAGTTGCGCTGCAGGGTCAACTATCATGCTTTAAGATTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16650.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 5
--------------------------gtaagactatgtcacctaagaatcaaattgttttagttact--ttatca-aatagaatcataggtattactattcatc--tttag-------ttttatcatctta-------tagctaattcatgtttgttgaaa--tcttgcagGTTTTACAATTGACAAAGTTTGACTACAGACTAGCAAATGATCTAGATGAAGACATGCAAAAGTTGCGCTGCAGGGTCAACTATCATGCTTTAAGATTCA
| ||| |||| | ||| ||| || || | | || || ||| ||| ||| | || || || ||||| | || | | | | | || | || | ||| | | ||||||||| | ||||||||||| |||||||| ||||| || ||| |||| ||||| || ||||||| || || ||| | || || ||||||||||| ||||| |
gtatatcttgatacatgtttgaaatttcttaattatttcactggaaaat-ggtttgattctgtgaatgactaccataatgaaatgttagttgttgcttaatgtcagtttagataattctcttgtaacttcggctgcattggttactgactgacttttgggatattttgcagGTTCTGCAATTGACAAAATTTGACTATAGACTTGCGAATAATCTTGATGATGAGCTGCAAAAATTACGTTGCCGTGTTAATTATCATGCTTTGAGATTTA
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G41740.1 (Glycine max), 3'ss of exon 5
-----------------------gtaagactatgtcacctaagaatcaaattgttttagttactttatcaaatagaatcat-aggtatta-ctattcatcttt---agttt------tatcatcttat-------agctaattcatgtttgttgaaatcttgcagGTTTTACAATTGACAAAGTTTGACTACAGACTAGCAAATGATCTAGATGAAGACATGCAAAAGTTGCGCTGCAGGGTCAACTATCATGCTTTAAGATTCA
|| || | ||| | | |||||| || || | || | ||||| | | |||| || | | ||| | ||| | || || || ||| | | | | ||||| || |||||| | ||||||||||| |||||||||||||| |||||| | || || | || | || || | || ||| | || || | ||||||||| ||||| |
gtatgaccagttgtttttgatacatattttaattttttttaattcactagatgttttgattcattaaataactctcatcatgaagcattagttactggtttttgtcaatttacagaatgtctctgaatttggctgagataactaacatgtag-gaaattttacagGTTGTTCAATTGACAAAATTTGACTACAGACTTGCAAATAACCTTGACAATGAGCTACAGAAACTACGTTGCCGCGTTAATTTTCATGCTTTGAGATTTA
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G03640.1 (Glycine max), 3'ss of exon 6
-------------------------------gtaagactatgtcacctaagaatcaaattgttttagttactttatcaaatagaatcataggtattactattcatc--ttta------gttttatcatctta------tagctaattcatgtttgttgaaatcttgcagGTTTTACAATTGACAAAGTTTGACTACAGACTAGCAAATGATCTAGATGAAGACATGCAAAAGTTGCGCTGCAGGGTCAACTATCATGCTTTAAGATTCA
|| |||| | | ||| || | | ||| | | | | ||| | || | || || |||| || | || | || |||| | | | | || || || |||||| | ||||||||||| |||||||||||||| |||||| | || ||||| || | ||||| | || ||| | || || | ||||||||| ||||| |
gtatagacacttgttatcgatacatatttgaacttttttaattcactagatgttttgattcattaaataactct-cctggtgaagcattagttgctagtttttgtcaatttacagaatgtctctgaatttggctgaggtaactaactaacatgtag-gagattttacagGTTGTTCAATTGACAAAATTTGACTACAGACTTGCAAATAACCTTGATGATGAGCTACAAAAACTACGTTGCCGCGTTAATTTTCATGCTTTGAGATTTA
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s0229g00100.t01 (Vitis vinifera), 3'ss of exon 5
gtaagactatgtcacctaagaatcaaattgttttagttactttatcaaatagaatcataggtattactattcatctttagttttatcatcttatagctaattcatgtttgttgaaatcttgcagGTTTTACAATTGACAAAGTTTGACTACAGACTAGCAAATGATCTAGATGAAGACATGCAAAAGTTGCGCTGCAGGGTCAACTATCATGCTTTAAGATTCA
| || ||| ||| | | || | || || | ||| | | | ||| ||| | || || |||| ||| || | |||| ||||||||| |||| |||||||||||||| ||||| || |||||| | | |||||||| ||||||||||||| ||| ||||||| |||||||||||||||||||
--------------------atgtaacttggttt--tcaagctagagtgatgtatt-tattttttattttgtaccttccaatttgttttcaatgaggcaattaatgctt-tgaaaattttgcagGTTGTACAGTTGACAAAGTTTGATTACAGGCTTGCAAATAACATTGATGAAGAGCTGCAAAAGTTGCGTTGCCGGGTCAATTATCATGCTTTAAGATTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatctttagttttatcatcttatagctaattcatgtttgttgaaatcttgcagGTTTTACAATTGACAAAGTTTGACTACAGACTAGCAAATGATCTAGATGAAGACATGCAAAAGTTGCGCTGCAGGGTCAACTATCATGCTTTAAGATTCA
agctaat putative branch site (score: 3)
ttttatcatcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagactatgtcacctaagaatcaaattgttttagttactttatcaaatagaatcataggtattactattcatctttagttttatcatcttatagctaattcatgtttgttgaaatcttgcagGTTTTACAATTGACAAAGTTTGACTACAGACTAGCAAATGATCTAGATGAAGACATGCAAAAGTTGCGCTGCAGGGTCAACTATCATGCTTTAAGATTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG