Sequence
atgc intronic sequence ATGC exonic sequencegttagtgttaaatgtcggtgtgtttcccaattttaattatctaattgtagttccaagttttactaaagagggtgtatgtgcccttgtttgaacctctgcagAAAGTGTTTTCGTTGATGTTGAGCCAATTCTAAGATCTGCAATGGACGGGCACAATGTGTGTGTTTTTGCTTACGGTCAAACAGGCACAGGCAAGACATT
Basic information
species | Glycine max |
transcript | GLYMA20G37340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g42800.1 (Oryza sativa), 3'ss of exon 1
----gttagtgtta--aatgtcggtgtgtttcccaattttaattatctaattgtagttccaagttttactaaagagggtgta---tgtgcccttgtttgaacctc-tgcagAAAGTGTTTTCGTTGATGTTGAGCCAATTCTAAGATCTGCAATGGACGGGCACAATGTGTGTGTTTTTGCTTACGGTCAAACAGGCACAGGCAAGACATT
||| | ||| | | || | || | | ||| | ||| | | | | ||| ||||| || | | ||| | | | |||| ||||||| || || |||||||||| ||||||||| | || ||||||||||| ||| || ||||||| |||||||| || ||||| ||||| |
gtatcttactcttactcacgagatctcgtcactgaacactgctattcttttcagttttcactgctcttattctgagagtgtaactcgtttcacttcttgttcataattcagAGGATGTTTTCCAAGAAGTGAAGCCAATTCTCAGATCTGCACTTGATGGGCACAATGTCTGTATTCTTGCTTATGGTCAAACTGGGACAGGAAAGACCTA
upper sequence: GLYMA20G37340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0030g01360.t01 (Vitis vinifera), 3'ss of exon 3
gttagtgttaaatgtcggtgtgttt--cccaattttaattatctaattgtagttccaagttttactaaagagggtgtatgtgcccttgtttgaacctctgcagAAAGTGTTTTCGTTGATGTTGAGCCAATTCTAAGATCTGCAATGGACGGGCACAATGTGTGTGTTTTTGCTTACGGTCAAACAGGCACAGGCAAGACATT
|| ||| | |||| || | ||||| | ||| ||||||||||| ||| | ||| | ||| || || || | | | | | | || || ||||| |||| |||||| ||||| || ||||||||||| || || ||| |||| ||||||||||| ||| | || ||||| |||||||| ||||| |||||||||||
gtcagtatcaaatctccatctgtttttctcaagtttaattatcttatttt-gtttccggttgtagta---agagactctatcctgcttttgaaaactctgtagAAGATGTTTTTGTTGAGGTCGAGCCAATTCTTAGGTCGGCACTGGATGGGCACAATGTATGTATATTAGCTTATGGTCAAACTGGCACTGGCAAGACATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagttccaagttttactaaagagggtgtatgtgcccttgtttgaacctctgcagAAAGTGTTTTCGTTGATGTTGAGCCAATTCTAAGATCTGCAATGGACGGGCACAATGTGTGTGTTTTTGCTTACGGTCAAACAGGCACAGGCAAGACATT
tactaaa putative branch site (score: 1)
cctctgc putative PPT
ttttactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgttaaatgtcggtgtgtttcccaattttaattatctaattgtagttccaagttttactaaagagggtgtatgtgcccttgtttgaacctctgcagAAAGTGTTTTCGTTGATGTTGAGCCAATTCTAAGATCTGCAATGGACGGGCACAATGTGTGTGTTTTTGCTTACGGTCAAACAGGCACAGGCAAGACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA