Sequence
atgc intronic sequence ATGC exonic sequence...atgaatttattctattatcatcattcatttggctattgttaatatctgatcaataatttctttttctttcacctattaatgacatttttaatggtattagTTTCATATGTCAAGAAGCTGAATATTCCAAGCGGTGTGGTGGGTGCCTGTCGTCTTGACCTAGCATATGAACATTTCAAG
Basic information
species | Glycine max |
transcript | GLYMA09G24090.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G24090.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G097959_T01 (Zea mays), 3'ss of exon 2
atgaatttattctattatcatcattca--tttggctattgttaa--tatctgatcaat---aatttctttttctttcacctattaatgacatttttaatggtattagTTTCATATGTCAAGAAGCTGAATATTCCAAGCGGTGTGGTGGGTGCCTGTCGTCTTGACCTAGCATATGAACATTTCAAG
||| | || | | | || ||| | || | ||| | | | | || | || | | ||||| | | | || | ||| || ||||| ||| || ||| | |||||||| ||||||| || ||||| ||||| ||||||||||||||||||||
-----ttttctataacaatgttctgcaaatttagtcatctccagcttatttagtgagtctgaaaggatgttcagcacttcagctaatgtggtctatcat--ttccagTATCCTATGTAAAGCGACTAAATGTGCCAAGCGGCATGGTGGGGGCTTGTCGCCTTGATGTAGCATATGAACATTTCAAG
upper sequence: GLYMA09G24090.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G62650.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------------------atgaatttattctattatcatcattcatttggctattgttaatatctgatcaataatttctttttctttcacctattaatgacatttttaatggtattagTTTCATATGTCAAGAAGCTGAATATTCCAAGCGGTGTGGTGGGTGCCTGTCGTCTTGACCTAGCATATGAACATTTCAAG
| || |||| || | ||| ||| || | || | | | | ||| | || || | | | | || || | | | |||||||||||| || || || ||||||||||| || ||||| || || ||||| ||||| | |||||||| |||||||||
gtgcattgacacttctctttgtaagctattttagcagtttccagtaacttagtctagatactacttgcttgtataagagccttctggttttgaataaggctgaaataatctaaaatga--attgcaatggagatcctgaaactgcaaacca-gattgccaatttttgggtc--ctgacg-tgttgtttgttttctcagTTTCATATGTTAAAAAACTAAATATTCCAAGTGGAGTGGTTGGGGCTTGTCGACTTGATTTGGCATATGAGCATTTCAAG
upper sequence: GLYMA09G24090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01470.t01 (Vitis vinifera), 3'ss of exon 2
atgaatttattctattatcatcattcatttggctattgttaatatctgatcaataatttctttttctttcacctattaatgacatttttaatggtat--------tagTTTCATATGTCAAGAAGCTGAATATTCCAAGCGGTGTGGTGGGTGCCTGTCGTCTTGACCTAGCATATGAACATTTCAAG
| | | |||| | | | | | || || || | ||||| ||| || ||| | || | ||||||||| | |||| | ||||| ||||| || |||||||| |||||||| |||| |||||||| ||||||||||| |||| |||| ||||||| |
-----tgttatgtattttatttgtctttataactgttttttaaccctgat---taagtttctttgaaactagtgatgactgacattttgattggtttcatttgtctagTTCGGTATGTTAAAAAGCTGAACATTCCAAGTGGTGGCGTGGGTGCATGTCGTCTTGATTTAGCTTATGGGCATTTCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatcaataatttctttttctttcacctattaatgacatttttaatggtattagTTTCATATGTCAAGAAGCTGAATATTCCAAGCGGTGTGGTGGGTGCCTGTCGTCTTGACCTAGCATATGAACATTTCAAG
tattaatgacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgaatttattctattatcatcattcatttggctattgttaatatctgatcaataatttctttttctttcacctattaatgacatttttaatggtattagTTTCATATGTCAAGAAGCTGAATATTCCAAGCGGTGTGGTGGGTGCCTGTCGTCTTGACCTAGCATATGAACATTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - -cattcat
- - - - - - - - - - - - - - - -gctattg