Sequence
atgc intronic sequence ATGC exonic sequencegtaaattttggtagagaatttcacttgatttcttcaattgattgtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
Basic information
species | Glycine max |
transcript | GLYMA04G01240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------gtaaattttggtagagaatttcacttgatt------tcttcaattgattgtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
|| |||| | || | | | || || | | | |||| ||||||||||| || ||||| ||||| || |||||||| |||||||| ||||| ||||| |||
ccaatccaaagtccaaaataaagtttgaagaactattatatgttaccatatatttagctaccaattctttattaatggaacaacatgtgctctttaacagAGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAG
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------------------------------------------------------------------gtaaattttggtagagaatttcacttgatttcttcaattgatt--gtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
|| |||| || | || || ||| | ||| || |||| ||||||||||||||||||||||||||| || || ||||| |||||||| ||||| ||||| |||
gtatatatttttcaaaatgaagatttcctttacaaataattgtattagtttgttctgtgggtatttccttccgtttctcagaagtttggttttatttgatgcattatgagtgaaattcaagtgaaaaaggaatattttttgtcaattc--atatgttagtttacacatttttattgtttgctttgatagAAAGTATTTTGGCGAGGGGTTGTTGAAGAACTGCTGTGGTTCATCAGTGGCTCAACAAATGCTAAG
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------gtaaat-tttggtagagaatttcacttgatttcttcaattgattgtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
| || || ||| | | || | || || | ||| |||||||||||||| |||| ||||||||||||||| | |||||||| ||||| ||||| ||||| |||
ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S34_360V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------gtaaattttggtagagaattt-----cacttgatttcttcaattgatt---gtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
|||| | | | |||| || | ||| | | | || | ||||| ||||| || ||||| || ||||| ||||||||||| |||||||| || |||||||||
caactattcgatataggtgtgaaactttctaccaactatattcttaggtatttacctgcgtgacctggaagtactttgattttgaaatgggtattggcagCGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaattttggtagagaatttcacttgatttcttcaattgattgtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
aattgat putative branch site (score: 4)
taaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattttggtagagaatttcacttgatttcttcaattgattgtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT