Sequence
atgc intronic sequence ATGC exonic sequence...ctgctgcttaagatccaactaatggaagagcttttgtgttaacattgacaacaggtgcctgtaattttctaaaggttctgttgaattatctctgatgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
Basic information
species | Glycine max |
transcript | GLYMA08G07870.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G07870.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
---ctgctgcttaagatccaactaatggaagagcttttgtgttaacattgacaacaggtgcctgtaattttctaaaggttctgttgaattatctctg-atgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
| || | || | || | | | || || ||| ||| | | | | | | | || ||| || ||||||||||||| |||||||| || |||||||||||||||||||| |||| || ||||| | || ||||| ||||| || || || |||||| ||||| | |
atgagaacatgcgtgctcgatctta-ggtatttcctctggtctagcatcagcaagacaactccctgcctagtgacaaaatagttt---ttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
upper sequence: GLYMA08G07870.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
--ctgctgcttaagatccaactaatggaagagctt-ttgtgttaacattga--caacaggtgcctgtaattttctaaaggttctgttgaattatctctg-atgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
|| | | | | | | || |||| |||| || ||| | ||| ||| | || || | ||| || || | ||||| ||||| |||||||| || |||| |||||||| ||||||||||| || ||||| | |||||||||||||| ||||| || |||||| | || | |
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctca------tgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
upper sequence: GLYMA08G07870.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
-------ctgctgcttaagatccaactaatggaagagcttttgtgttaacattgacaacaggtgcctgtaat--tttctaaaggttctgttgaattatctctgatgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
| || ||| | || | | | || | || || | ||| |||||| || | || || | | || | | | | ||||||||||| |||||||| |||||||||||| | ||||||||| ||||||| ||||| | |||||||||||||| ||||| ||||||||| | || |||
ttgttaaattctttttacaaccctgtttctatcaag---ttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtg------ggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacaacaggtgcctgtaattttctaaaggttctgttgaattatctctgatgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
ttatctct CT-rich tract
tgtaattttctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgctgcttaagatccaactaatggaagagcttttgtgttaacattgacaacaggtgcctgtaattttctaaaggttctgttgaattatctctgatgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
ctgctgc
- - - - - - - ccaacta
- - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - -caggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttg