Sequence
atgc intronic sequence ATGC exonic sequencegtatgatgcaatcaccttttgcgctcatgctttctaataaagattgtttaaacttagtagttttggtttgcgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
Basic information
species | Glycine max |
transcript | GLYMA03G39260.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g49040.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------gtatgatgcaatcaccttttgcgctcatgctttctaataaagat----tgtttaa--acttagtagttttggtttgcgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
| |||||| | | | || || || | || ||||| | | | | ||| || | | |||| |||||||| ||||| || |||||||||||||| ||||||| || ||||| || || |||| |||||| || || || |||||||| || |||||||| ||||
gtaccaattcgccccgcagtttggtagatgatggccagattgaaaaaaagagaggcttcgcttttgcgatgca-ttgctatgtgaagctttgtttccagtcggccatgttctgttttgtgatgcattgttgttgtttgatgctttgttc-tagGTTGGTCCTCTCCGGTGCTGGCCAGGTGGCCTGTGCCTTTCAAGATCTATCGGGGACATGGATGTCGGGGAGTTCATTGTGCCGATTCCACATGTGAAGC
upper sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
---------------gtatgat--gcaatcaccttttgcgctcatgct-ttctaataaagattgtttaaacttagtagttttggtttg------cgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
||| | | || || | | ||| | | || |||| | | | | ||| |||||| | || | | | || ||||| || ||||| | ||||||||||||||||||||||| || ||||| || || || || || || || || || ||||||||||| |||||||| ||||
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctca--ttatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
upper sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
---------------------gtatgatgcaatcaccttttgcgct----catgctttctaa---taaagattgtttaaacttagtagttttggtttgcgttat---gtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
| ||||| | || | | | ||| |||| | | ||| | | | | |||| || || | ||| ||||| || ||||| || ||||||||||||||||||||||| || || ||||| || || || ||||| || || || ||||| || || |||||||| ||||
gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
upper sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G09160.2 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------gtatgatgcaatcaccttttg--cgctcatgctttctaat----aaagattgtttaaactt--agtagttttggtttgc----gttatgtttat-----agGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
|| | || ||||| | | ||| |||| || | | || | || | | | || | ||| ||||| || |||| || || || || |||||||| ||||| || || || || || || || || || ||||||||||||||||||||||| || |||||||| || ||||
gtatgatcatttccagtgaatttaagttactgtttcattgtgttttggctgtggtgggtttgtaatgtgtaagaagtccttggattttcaatgatattaatgtgctttgattatgccaatgcaatagGTCGGCCCACTACGATGCTGGCCTGGTGGTTTATGTCTTTCGAGGTCCATTGGTGATACGGATGTGGGAGAATTTATTGTCCCTATACCACACGTTAAGC
upper sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
---------gtatgatgcaatcaccttttgc-gctcatgc---tttctaataaagattgtttaaactt-agtagttttggtt----tgcgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
| |||||| || | ||| | ||| | | | ||| | ||| | | | ||| | || | |||| |||||||| || || ||||||||||| |||||||| || || ||||| ||||| || ||||| |||||||||||||| ||||| |||||||||||||| ||||
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctaataaagattgtttaaacttagtagttttggtttgcgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
ttctaat putative branch site (score: 2)
taataaagattgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatgcaatcaccttttgcgctcatgctttctaataaagattgtttaaacttagtagttttggtttgcgttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA