Sequence
atgc intronic sequence ATGC exonic sequencegtatgattttgatgagtctcaatttaaacaataatgtatgttacaattctcaaatcctgactattttttttgttattctttgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05520.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05520.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA07G39450.1 (Glycine max), 3'ss of exon 14
--------------gtatgattttgatgagtctcaatttaaacaa-taatgtatgtt-acaat-tctcaaatcctga---ctattttttttgttattctttgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
|| || || |||||| | || | |||| |||| | ||| | || | || | || | |||||| ||| | |||||| ||||| |||||||| || ||| ||||||| || || ||||||| ||||| ||||| |||| ||| || ||||| ||||||||||||||| | ||
gtatggtcctattttcataatatttatgagtaatgctatatcctcctaattcttgtttataatatatctggttctaaaatctgatgtttttggaattgt--gcagATCAATGAATTTGTGAAACGTGCTAGATCTGCTAAAATTCATGCATATATAATTAGTCATCTTAGGAATGAGATGCCTGCAATGATGGGCAAAGCTAAGA
upper sequence: AT4G05520.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA17G01310.1 (Glycine max), 3'ss of exon 14
---------------------------------------------------------------------------------gtatgattttgatgagtctcaa---tttaaacaataatgtatgttacaattctc--aaatcctgactattttttttgttattctt-------------------tgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
||| || || | | || | | |||||| | | | | | ||| ||| || || || ||| | | | | |||| ||||||| ||||| |||||||| || || ||||||| || || ||||||| ||||| ||||| |||| ||| || ||||| ||||||||||||||| | ||
gtatggtcctattttgataatattgtttgacctggtaatgcaaatgggtgaattatgtgcatatggcagatcactgcaatcttatatttacgagtaatgccatatcctcatacaata-tctttctaataatcctcctaattcttgtttataatatatctggttctaaaatctgatgttggaatcgtgcagATCAATGAATTTGTGAAACGTGCCAGATCTGCTAAAATTCATGCATATATAATTAGTCATCTTAGGAATGAGATGCCGGCAATGATGGGCAAAGCTAAGA
upper sequence: AT4G05520.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G01160.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------------------gtatgattttgatgagtctcaatttaaa--caataatgtatgttacaattctcaaatcctgactattttttttgttattctttgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
||| || || ||| | | | ||| || || | || || | ||| | | ||||||| ||||| |||||||| || || ||||||| || || ||||||| ||||| || || ||||||||||| ||||| || || ||||||||| |||| |
gtattgtcaataatttcatattatttgggacatggtagtgaaaattgaattaattttatgtggatgatagaccactgaattacctgtacctcgtgtcagctcctatatattaatttcctgtttcaaagatttagtcattggaaatttggaatggtgcagATCAATGAATTTGTGAAACGTGCAAGATCTGCTAAAATTCATGCATATATAATTAGCCATCTTAAGAAGGAGATGCCTGCTATAATGGGCAAAGCCAAGG
upper sequence: AT4G05520.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G11970.1 (Glycine max), 3'ss of exon 13
--------------------------------------------------------------------------gtatgattttgatgagtctcaatttaaacaata-atgtatgttacaattctcaaatcctgactattttttttgttattctttgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
||| || | || |||| | | || || | ||| | | ||||| | ||| | | ||||||| ||||| ||||| || || || ||||||| || || ||||||| ||||| ||||||||||||||||| ||||| || || ||||| ||| |||| |
gtatggtcaataatttcatattatttgtgtggcctggtggtgaaaattgaattagttttatgtagatggcagaccactgaattagttgtatctcgtgtcagctcctatattttagtttcctgtttcaaacattagtcattggaaatttggaatggtgcagATCAATGAATTTGTCAAACGTGCAAGATCTGCTAAAATTCATGCATATATAATTAGTCACCTTAAGAAGGAGATGCCTGCTATAATGGGTAAAGCCAAGG
upper sequence: AT4G05520.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv00s0516g00020.t01 (Vitis vinifera), 3'ss of exon 15
gtatgattttgatgagtctcaatttaaacaataatgtatgttacaattctcaaatcctgactattttttttgttattctttgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
| | | | | ||||| ||| | || | || | | | || | | | | || | |||||||| ||||| ||||| || |||||| || |||| ||||| |||| || ||||| |||||||| || ||||| ||||| ||||||||||||||| | ||||
--gtaagctc-accattctcatttt------ttatctgctttctgagtgttaag-cagaattctgacagcatttgtatattgcagATCAATGAATTTGTAAAACGAGCTAGAGCTGCCAAGATTCATGCCTATATAATCAGTCACCTCAAAAAGGAGATGCCTGCAATGATGGGCAAAGCTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatgtatgttacaattctcaaatcctgactattttttttgttattctttgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
tcctgac putative branch site (score: 2)
ctattttttttgttat CT-rich tract
actattttttttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattttgatgagtctcaatttaaacaataatgtatgttacaattctcaaatcctgactattttttttgttattctttgcagATTAATGAGTTTGTGAAGCGAGCTCGATCTGCAAAGATAAATGCATACATAATGAGTCACCTTAAGAAGGAAATGCCAGCAATGATGGGCAAATCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA