Sequence
atgc intronic sequence ATGC exonic sequencegtaatcttagttgaataagatattttgctttgaatagtatgaaatgtataaacacggctcttaactacagaacacatttcgtctactgttctagGTTAGTGCTCTTCATAATGTTGAGGCCAAGAAGAGATTTGATTTTTTGGAGGCTGTCACTGGAGTTATGGATGCTCATCTTCGGTATTATCGACAG
Basic information
species | Glycine max |
transcript | GLYMA04G37780.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 8
----gtaatcttagttgaataagatattttgctttgaatagtatgaaatgta----taaacacggctcttaactacagaacacatttcgtctactgttctagGTTAGTGCTCTTCATAATGTTGAGGCCAAGAAGAGATTTGATTTTTTGGAGGCTGTCACTGGAGTTATGGATGCTCATCTTCGGTATTATCGACAG
|| | |||||| | ||| || | ||| | | | ||| | | | | | | || | | ||| | || ||||| | | | || || ||||||| |||||||||||||| |||||||||||||| | | | ||||||| |||||||||| |||| | |||
gtatgtgaaac-agttga-tcagactttgttcttgtattttcttactgtgtgccttttttcttatcatatcatcatttgccatacctgcactatt-ttttagGTCACTTCAATTTCCCATATTGAGGCAAAGAAGAGATTTGAATTTTTGGAGGCTGTTAGTTCAACTATGGATTCTCATCTTCGATATTTTAAACAA
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 8
--gtaatcttagttgaataagatattttgctttgaatagtatgaaatgtataaacacggctcttaactacagaacacatttcgtctactgttctagGTTAGTGCTCTTCATAATGTTGAGGCCAAGAAGAGATTTGATTTTTTGGAGGCTGTCACTGGAGTTATGGATGCTCATCTTCGGTATTATCGACAG
| | ||| ||| | | | ||| | | | | ||||| || | || || | |||| | || |||| | ||| ||| ||| | ||||||||||| |||||||| ||||| |||||||||| ||| |||||||| ||||| || |||| |||
gtacatgcactgtttccctgtataact-gttctgatttctgt-agttgtatgtaccgtggctttgtctt----atctatttaat------tttcagGTGACTGCACTTTCAAATATCGAGGCCAAGAAAAGATTTGAATTTTTAGAGGCTGTCAGTGGGACAATGGATGCACATCTGCGCTATTTCAAACAA
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 5
gtaatcttagttgaataagatattttgctttgaatagtatgaaatgtataaacacggctcttaactacagaacacatttcgtctactgttctagGTTAGTGCTCTTCATAATGTTGAGGCCAAGAAGAGATTTGATTTTTTGGAGGCTGTCACTGGAGTTATGGATGCTCATCTTCGGTATTATCGACAG
||| || | | || ||||||| | | ||| | |||| | | | | || || || | | |||| | | | ||| |||| ||||| |||||||||||||| |||||||||||||| | || |||||| | |||||||| |||| | |||
gtatgatttgcatcgtcccttactttgcttcttagtttctgagct-tatatgcttatcatgccattgtttgtcatatccatgttaatttctcagGTCACTTCACTTTCCCATGTCGAGGCAAAGAAGAGATTTGAATTTTTGGAGGCTGTTAGTGCGACAATGGATTCACATCTTCGTTATTTTAAACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaatgtataaacacggctcttaactacagaacacatttcgtctactgttctagGTTAGTGCTCTTCATAATGTTGAGGCCAAGAAGAGATTTGATTTTTTGGAGGCTGTCACTGGAGTTATGGATGCTCATCTTCGGTATTATCGACAG
tcttaac putative branch site (score: 2)
ctgttct putative PPT
tgtataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcttagttgaataagatattttgctttgaatagtatgaaatgtataaacacggctcttaactacagaacacatttcgtctactgttctagGTTAGTGCTCTTCATAATGTTGAGGCCAAGAAGAGATTTGATTTTTTGGAGGCTGTCACTGGAGTTATGGATGCTCATCTTCGGTATTATCGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG