Sequence
atgc intronic sequence ATGC exonic sequence...cattttcattattttttttgttttgttcagttatcatttgctatgcattattcttgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTTTTCATGTTTGTCTTCTCAACTACGCTATTGTGTATATACATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGC
Basic information
species | Glycine max |
transcript | GLYMA01G08200.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G08200.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------cattttcattattttttttgttttgttcagttatcatttgctatgcattattcttgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTTTTCATGTTTGTCTTCTCAACTACGCTATTGTGTATATACATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGC--
||| | | | |||| ||| | || ||| | || || | |||| || | || | |||||| | | ||| |||||||||||||||||||||| | ||||||||| ||||| || ||| || | || | ||| | ||| || || || ||||| || || | | ||||
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgt-atttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgag---cctaatca-taaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTT--GCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
upper sequence: GLYMA01G08200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 3
cattttcattattttttttgttttgttcagttatcatttgctatgcattattcttgaatataca--ttatgtat---cctaattgcttgcacgattttta-tgcagCGTAATTATCGGTTCTTTTTCATGTTTGTCTTCTCAACTACGCTATTGTGTATATACATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGC--
|| | || | | || | | | |||||| | ||||||| | ||| || || | ||| ||| ||| | |||||||||||||||| || || ||||||||||||||||| || || || | |||||||| ||||| | || ||||||||||||||| || || ||||
----ttttccagttgtcat-cttcaccaacatgataggaatgatgcat-gtgcttgaatttgtgggcaatgcatgaatctgaacactttcacaattctgggtgcagCGTAATTATCGATTTTTCTTCATGTTTGTCTTCTCGACGACTCTTCTTTGTATATATGTGTTT--GGGTTCTGCTGGGTCTATATTAAGAGGATCATGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattattcttgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTTTTCATGTTTGTCTTCTCAACTACGCTATTGTGTATATACATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGC
tcctaat putative branch site (score: 2)
tttttat putative PPT
aatatacattatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattttcattattttttttgttttgttcagttatcatttgctatgcattattcttgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTTTTCATGTTTGTCTTCTCAACTACGCTATTGTGTATATACATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGC
- - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgca