Sequence
atgc intronic sequence ATGC exonic sequencegtaatttccaatgtgcaagatagaagattgctttaaaagatcaaatctttcttacggagactcttaacatgtctttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36210.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36210.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 11
------------------gtaatttccaatgtgcaagatagaagattgctttaaaagatcaaatctttcttacggagactcttaacatgtct-ttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
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ggttattttacatattatatcatttctatggggactcgtgcgtttatctgttaaataagatgttcccttattctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG
upper sequence: AT4G36210.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G07870.1 (Glycine max), 3'ss of exon 10
---------gtaatttccaatgtgcaagatagaagattgctt--taaa--agatcaaatctttctta------cggagactcttaacatgtct-ttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
| ||||| || | | | | || | |||| |||| |||||||| | ||| | || ||| | |||| ||||||||| || ||||||||||||||||||||| ||||||| ||||||| ||| || ||| || | || |||
agatattatatgatttctg-tgggggaatcatgcgtttatctgttaaataagatgttccctttcttattgattccgaggcactgcttctgtttattggcagCTGAACTGGTCGAGAGAGTTGTTCTTCTTGGATTACCCATTGCAATCAAGGATGAGAATTGGGAAGCTGCTAGAAAG
upper sequence: AT4G36210.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 11
----------------gtaatttccaatgtg--caagatagaagattgctttaaaagatcaaatctttcttacggagact-cttaacatgtctttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
|||| ||| | | || | | ||| | | | | | || || ||| | || | | | | ||| |||||||||||| || | |||||| ||||||||||||||||| |||||| ||| |||||| || || |||
gatggatgcatataatttaatgtcccttcttttcatgtttatccgttgaatgagacgttaccatattacttttaatgtctgccctgcttattattgacagCTGAACTTGTAGAAAAAGTTGTACTTCTTGGAGCACCCATCCCAATCATGGATGAGAACTGGGAAGCAACTAGAAAG
upper sequence: AT4G36210.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
gtaatttccaatgtgcaagatagaagattgctttaaaagatcaaatctttcttacggagactcttaacatgtctttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
|||| | | | |||| | | ||| | | | | | ||| || | ||| | |||| |||||||||||| || ||||||||||||||||||||||||||||| ||| ||| |||||| || | || ||
gtaactggtaccct-caagct----gtttgtgatggatggtttgtattgcattaatgatgtgatacacaaatttttg-cagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgctttaaaagatcaaatctttcttacggagactcttaacatgtctttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
tcttaac putative branch site (score: 2)
tgtcttt CT-rich tract
tttaaaagatcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttccaatgtgcaagatagaagattgctttaaaagatcaaatctttcttacggagactcttaacatgtctttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA