Sequence
atgc intronic sequence ATGC exonic sequence...gattgcataagttccaacccatgaaagagcttttgcgttaagattgacagcagggtgtctgtaattttctaaaggttctgttgaattatctttaatgcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
Basic information
| species | Glycine max |
| transcript | GLYMA05G24650.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G24650.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
--gattgcataagt-tccaacccatgaaagagcttttgcgttaagattgacagcagggtgtctgtaattttctaaaggttctgttgaattatctttaat--gcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
|| ||| || | | | | | | | || || || ||||| | || | ||| | | | || | || || ||||||||| || || ||||| || ||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| || || || |||||| ||||| | |
atgagaacatgcgtgctcgatcttaggtatttcctctggtctagcat---cagcaagacaactcc--ctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
upper sequence: GLYMA05G24650.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
----gattgcataagttccaacccatgaaagagcttttgcgttaagattga-cagcagggtgtctgtaattttctaaaggttctgttgaattatcttta-atgcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
|| ||| | | || | ||| || || | || |||| | || || | ||| || ||||| ||||| || || || ||||| || |||| ||||||||||||||| |||| || ||||| || |||||||||||||| ||||| || |||||| | || | |
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctca------tgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
upper sequence: GLYMA05G24650.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
gattgcataagttccaacccatgaaagagcttttgcgttaagattgacagcagggtgtctgtaattt---tctaaaggtt-ctgttgaat-tatct--ttaatgcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
||| ||| ||| | | | || || | | | || || || | | || | |||| || ||| |||| | | | | |||||||| || || ||||| |||||||||||| | || |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||| | || |||
--ttgt-taaattc----tttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacagcagggtgtctgtaattttctaaaggttctgttgaattatctttaatgcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
ttatcttt CT-rich tract
ttgaattatctttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattgcataagttccaacccatgaaagagcttttgcgttaagattgacagcagggtgtctgtaattttctaaaggttctgttgaattatctttaatgcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- -tgcataa
- - - - - - -ccaaccc
- - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttg
