Sequence
atgc intronic sequence ATGC exonic sequence...atatattttaaactttctattgtttgtttattttatcacatttctttgtctagtaattagcatgttttcaatttttaattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
Basic information
species | Glycine max |
transcript | GLYMA14G04110.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G04110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
---------------------atatattttaa-actttctattgtttgtttattttat-cacatttctttgtctagtaattagcatgttttcaatttttaattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
|||| | || | | | || | | || | | || | | || || | | | || | ||||| | | || | ||| || | | |||| |||||| |||||||| |||||||| ||| |||| || | |||||||||||||| | ||| || |||||||| |||||||
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
upper sequence: GLYMA14G04110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 3
------atatattttaaactttctattgtttgtttatttt-atcacatttctttgtctagtaattagcatgttttcaatttttaattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
| ||| | ||| | | || | ||| | ||| | | || | | | ||| | | || | ||||| | | || | ||| || | | |||| |||||| |||||||| |||||||| ||| |||| || | |||||||||||||| | ||| || |||||||| |||||||
ataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattacc-acaagtta------ctccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
upper sequence: GLYMA14G04110.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------------------------atatattttaaactttctattgtttgtttattttatcacatttctttgtctagtaattagcatgttttcaatttt----taattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
| | | | | || | || || ||| | || | | ||||| | | | | | ||||| | || | || || | || || | || |||||||||||||||| ||||| ||||||||||||||||| ||||| | || |||||||| || || || || |||||||| ||| | |
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtt-taaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
upper sequence: GLYMA14G04110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 2
-----atata-ttttaaactttctattgtttgtttattttatcacatttctttgtctagtaattagcatgttttcaatttttaattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
||||| |||| | ||| | | ||||| || | || || ||| | ||| | |||| |||| || | | | || || ||||||| | |||||||||||||||| |||||||| ||||||||||||||||||||||| |||||||||||||| ||||| |||||| |||| || | |
taataatataattttgcattttacaatctttgtg---ttactggagttgtttcatctgat--ttattttattttatgttttatttttgtactttgataaga-gcagTTTTTAGGAGGTATACCAAAGTTTGTGAAGATAGTGGAAGTTGGTCCAAGGGATGGATTGCAAAATGAGAAGAATATTGTACCTACAGCTGTAAAAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtctagtaattagcatgttttcaatttttaattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
ttttaat putative branch site (score: 3)
taattagcatgttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatattttaaactttctattgtttgtttattttatcacatttctttgtctagtaattagcatgttttcaatttttaattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt