Sequence
atgc intronic sequence ATGC exonic sequencegtaagtccattgctatgaacaatttcactttctttctaaaagtttcgttcattcatgatttggtgaagaaaatattgcgcctttgcagTGGCCGAAGCAGTTGAATGCTTCACTTGAGGTCGTTGATCCTGAGATTGCTGATATTATTGAGCTTGAGAAAGCTAGGCAATGGAAG
Basic information
species | Glycine max |
transcript | GLYMA18G27710.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 2
--------gtaagtccattgcta--tgaacaatttcactttctttctaaaagtttcgttcattcatgatttggtgaagaaaatattgcgcctt----tgcagTGGCCGAAGCAGTTGAATGCTTCACTTGAGGTCGTTGATCCTGAGATTGCTGATATTATTGAGCTTGAGAAAGCTAGGCAATGGAAG
| ||| | | ||| |||| ||| | || || || || || | | | || | | | |||||||| ||||||||||||||| | || | ||| || |||||||| ||||| || ||||| ||||| |||||||| || |||||||||
gtaagcgaattagtttttcatttattgatttttttctcttctctcctggaatgtttattatgtcgtttcaccttatttgttctgttctggtataaatttcagTGGCCAAAGCAGTTGAATGCTCCGCTGGGGGTTGTGGATCCTGAAATTGCAGACATTATAGAGCTCGAGAAAGCAAGACAATGGAAG
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 2
--------gtaagtccattgct-atgaacaattt--cactttctttctaaaagtttcgttcattcatgatttggtgaagaaaatattgcgcctt----tgcagTGGCCGAAGCAGTTGAATGCTTCACTTGAGGTCGTTGATCCTGAGATTGCTGATATTATTGAGCTTGAGAAAGCTAGGCAATGGAAG
| ||| | | || | ||| | ||| | || || || || || | | | | || | | | |||||||| ||||||||||||||| | || | ||| || |||||||| ||||| || ||||||||||| |||||||| || |||||||||
gtaagcgaattagtttttcatttattgattttttttctcttctctcctggaatgtttattatgtcgtttcatcttatttgttctgttctggtataaatttcagTGGCCAAAGCAGTTGAATGCTCCGCTGGGGGTTGTGGATCCTGAAATTGCAGACATTATTGAGCTCGAGAAAGCAAGACAATGGAAG
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 2
------------gtaagtccattgctatgaacaatttcactttctttctaaaagtttcgttcattcatgatttggtgaagaaaatattgcgcctt----tgcagTGGCCGAAGCAGTTGAATGCTTCACTTGAGGTCGTTGATCCTGAGATTGCTGATATTATTGAGCTTGAGAAAGCTAGGCAATGGAAG
|| || || | |||| ||| | || || || || || | | | | || | | | |||||||| ||||||||||||||| | || | ||| || |||||||| ||||| || ||||||||||| |||||||| || |||||||||
gtaagcgaattagtttttcatttattgatttttttttctcttctctcctggaatgtttattatgtcgtttcatcttatttgttctgttctggtataaatttcagTGGCCAAAGCAGTTGAATGCTCCGCTGGGGGTTGTGGATCCTGAAATTGCAGACATTATTGAGCTCGAGAAAGCAAGACAATGGAAG
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 2
--------gtaagtccattgcta--tgaacaatttcactttctttctaaaagtttcgttcattcatgatttggtgaagaaaatattgcgcctt----tgcagTGGCCGAAGCAGTTGAATGCTTCACTTGAGGTCGTTGATCCTGAGATTGCTGATATTATTGAGCTTGAGAAAGCTAGGCAATGGAAG
| ||| | | ||| |||| ||| | || || || || || | | | || | | | |||||||| ||||||||||||||| | || | ||| || |||||||| ||||| || ||||| ||||| |||||||| || |||||||||
gtaagcgaattagtttttcatttattgatttttttctcttctctcctggaatgttaattatgtcgtttcaccttatttgttctgttctggtataaatttcagTGGCCAAAGCAGTTGAATGCTCCGCTGGGGGTTGTGGATCCTGAAATTGCAGACATTATAGAGCTCGAGAAAGCAAGACAATGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctaaaagtttcgttcattcatgatttggtgaagaaaatattgcgcctttgcagTGGCCGAAGCAGTTGAATGCTTCACTTGAGGTCGTTGATCCTGAGATTGCTGATATTATTGAGCTTGAGAAAGCTAGGCAATGGAAG
ttctaaa putative branch site (score: 2)
cgccttt putative PPT
aagaaaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtccattgctatgaacaatttcactttctttctaaaagtttcgttcattcatgatttggtgaagaaaatattgcgcctttgcagTGGCCGAAGCAGTTGAATGCTTCACTTGAGGTCGTTGATCCTGAGATTGCTGATATTATTGAGCTTGAGAAAGCTAGGCAATGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG