Sequence
atgc intronic sequence ATGC exonic sequencegtaagagacaacatatctcctttatgatttcacttgtgttctgttgagtaacaagaaatgatgattaaaatggttatagGAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28640.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G40930.2 (Glycine max), 3'ss of exon 2
---------------------gtaagagacaacat-atctcctttatgatttcacttgtgttctgttga-gtaacaagaaatgatgattaaaatggttatagGAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAG
||| || | ||| | | | | | | |||| || ||||| || | | || | | || | || ||||| |||||||||||||| | || || |||||| ||||||||||||| |||||||| || || ||||| | ||| | | |||
ctttcactcaaaaactgggcacaaagggatgttaagatcccatatcagctataacttttgga--gttgatgttagaccaagttcgtgctcaatttttttcagGAACCAAGCAAGGCTTCAGAGAAATCTCATGTACTTAGCTGCAATAGCTGATTCTCAACCCCAACCACCCACCATGCCTGGTCAG
upper sequence: AT5G28640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G43580.1 (Glycine max), 3'ss of exon 2
--------------------gtaagagacaacatatctcctttatgatttcacttgtgttctgttga-gtaacaagaaatgatgattaaaatggttatagGAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAG
||| | | ||| ||| | || | | |||||| || | | || | | || | || ||||| |||||||||||||| | || || |||||| ||||||||||||| |||||||| || || ||||| | || | | |||
tacgtcacccaaaactgggcataaagggatgttaagatcccatatcagttataccttttggtgttgatgttagaccaagttcatgctcaatttttttcagGAACCAAGCAAGGCTTCAGAGAAATCTCATGTACTTAGCTGCAATAGCTGATTCTCAACCCCAACCACCCACCATGTCTGGTCAG
upper sequence: AT5G28640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G36960.1 (Glycine max), 3'ss of exon 2
---------------------gtaagagacaacatatctcctttatgatttcacttgtgttctgttgagtaaca-agaaatgatgattaaaatggttat-agGAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAG
| ||| | | | ||| | | || |||| || | | | || | ||| || | || | ||||| ||| ||||||| || | || || |||||||||||||||||||| |||||||| || || ||| | ||| | | |||
ttattggatttttctcttaacatcagattct-cgttcctctcctgttccttttactgtggtcc-taaaacatcatattaatcatcctcttgccatttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG
upper sequence: AT5G28640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30650.1 (Glycine max), 3'ss of exon 2
-----------------gtaagagacaacatatctcctttatgatttcacttgtgttctg-ttgagtaacaaga-aatgatgat--taaaatggttatagGAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAG
| || || | || | | | | | ||| || | || | |||| | |||||| | | || || ||||| ||| ||||||| || | || || |||||||||||||||||||| |||||||| || || ||| | || | | |||
gattttgcccttaacatcttagcatcagattctcgctcctcttctgttccttttgctgtggtcctaaaacatcataatgatcctcttgtcattatttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGATTCTCAACCACAACCATCTCCATTGGCTGGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatttcacttgtgttctgttgagtaacaagaaatgatgattaaaatggttatagGAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAG
gagtaac putative branch site (score: 2)
aaatgatgattaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagacaacatatctcctttatgatttcacttgtgttctgttgagtaacaagaaatgatgattaaaatggttatagGAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT