Sequence
atgc intronic sequence ATGC exonic sequence...aatgacatcgtgtagtccttgtagctgacttcacttagtgaaataaagattcatttgttgttagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
Basic information
species | Glycine max |
transcript | GLYMA15G05240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G05240.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
aatgacatcgtgtagtccttgtagctgacttcacttagtgaaataaagattcatttgttgt-------tagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
|| | | |||||| || | || |||||| | | || | ||| || ||| | ||||||| || || ||| | | | ||| ||||| || ||| |||||||||||| |||||| |||||||||| ||||||||||| ||| |||| |||||||| |||||||||||||
----gaatgatatcttccttggagataacagtttgcagtgaatctattttgcaccgatcagaaaagagtagctttgtgaatttttatttcatgtttc---attacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
upper sequence: GLYMA15G05240.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S309_83V6.1 (Physcomitrella patens), 3'ss of exon 1
--aatgacatcgtgtagtcct--tgtagctgacttcacttagtgaaata---aagattcatttgttgttagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
|| ||| || | | ||| | || | || || | | | | | | ||| | || |||||| | || ||| | ||||| | || |||| || ||||| |||| |||||||| || | | |||| ||||||||||||||||| |||||||| || ||||| || ||||| | ||
cttatcctttcgcttaaatgtgatctaggtt-ctgcgtttggtaatttgcgtaggtctaagttggtcaaggtggttggaa------tggcaacgtttgggtgtgcagGTGGAACTTGGTGGTGGTGGTGGAGGTATTGGAAATAAGAATTTTAATGGGGGTGGTGATGGAGGTGACGATGATGGCGACGATGATGACTACTTCGGTG
upper sequence: GLYMA15G05240.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S57_231V6.1 (Physcomitrella patens), 3'ss of exon 1
aatgacatcgtgtagtccttgtagctgacttcacttagtgaaataaagattcatttgttgttagtatttggaaatccattt--tcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
| | || | | | || || ||| | || ||| | | | ||| || || | | | || | | ||| ||||| |||| | || |||| || ||||| || | ||||| || || | |||| ||||| |||||||||||||||||||| ||||||||||| ||||||| ||
-aagttctccctttttggataaagttgtcttagggttttgttttaagattgcttgatttggcagggcgtgaacgtggagttgatgagacttgtaatt-gcagGTGGAACTTGGAGGCGGTGGTGGCGGTATTGGGAATAAGAATTTCAATGGAGGTGGAGATGGAGGTGATGATGATGGCGATGATGACGACTACTTTGGTG
upper sequence: GLYMA15G05240.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S4_62V6.2 (Physcomitrella patens), 3'ss of exon 1
---aatgacatcgtgtagtccttgtagctgacttcacttagtgaaataaagattcatttg--ttgttagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
|| | || | | | | || | || | | | || ||| ||| | | || | | | ||| | | | | |||| || | || | || | || || ||||| |||| ||||| || || | | |||| ||||| || |||||||| |||||||| ||||||||||| ||||||| ||
gtggatagcctcaacctttggataaggttaacct-acggttttaggtttggagtcacttggctcgctatttgcttggaattga---tgacgattttggtt-gtagGTGGAGCTCGGAGGTGGTGGCGGAGGAATTGGTAATAAGAACTTCAATGGGGGTGGCGACGGAGGTGACGATGATGGTGATGATGACGACTACTTTGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagattcatttgttgttagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
ttttaat putative branch site (score: 3)
tgctttt CT-rich tract
ttttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgacatcgtgtagtccttgtagctgacttcacttagtgaaataaagattcatttgttgttagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- tgacatc
- - - - - - - - ccttgta
- - - - - - - - - - - -gctgact
- - - - - - - - - - - - - - - - -cttagtg
- - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt