Sequence
atgc intronic sequence ATGC exonic sequence...aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaacttttatttggaatcataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
Basic information
species | Glycine max |
transcript | GLYMA07G39690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g53750.1 (Oryza sativa), 3'ss of exon 2
aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaacttttatttgga--atcataatttatttgtct-ggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
|| |||||| | | | | |||| || ||| || | || | | | || | | | ||||| ||| | ||||||||||| ||||||||||| ||||||||||| |||| ||| || | | || || || | || || || || || || |
----------------gt-tttctttactaccttgcactgttcattcaatcagcagcttgtccaaatccaaataatgctgactgtttcattttaatcccatagTGGTTGCATAACATCAGCAGAAACAGTTATGCTTGAGAAGCAAAGCTTGGGTGACTTCATTACTCGCATCAACTCTGACAAAGCTGTCATAGTATCGGTC
upper sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g53750.2 (Oryza sativa), 3'ss of exon 2
aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaacttttatttgg--aatcataatttatttgtct-ggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT-----------------
|| |||||| | | | | |||| || ||| || ||| | | | || | | | ||||| ||| | ||||||||||| ||||||||||| ||||||||||| |||| ||| || | | || || || | || || || || || || |
----------------gt-tttctttactaccttgcactgttcattcaatcagcagcttgtccaaatccaaataatgctgactgtttcattttaatcccatagtggttgcataacatcagCAGAAACAGTTATGCTTGAGAAGCAAAGCTTGGGTGACTTCATTACTCGCATCAACTCTGACAAAGCTGTCATAGTATCGGTCTCTCCACAGTCAAGAGC
upper sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171998_T01 (Zea mays), 3'ss of exon 2
aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaacttttatttggaatcataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
|||| | || ||| | ||| || | ||| | | |||| ||| || | | || ||| | | | ||| ||| | ||||| || | ||||| |||||||| |||||||||||||||||||| |||| ||| || | | ||| || || | || || || ||||| ||| |
--gtttttcttttattttctttttttactcttttgatcagttgtcaataagtaacctgatcaatttcaatcaatgctgactgattcatctt-tgtcttagTGGTTGTATAACATCGGCAGAGACGGTTATGCTGGAGAAGCAAAGCTTGGGTGACTTCATTGATCGTATAAACTCTGATAAAGCTGTTATTGTATCTGTA
upper sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G456690_T01 (Zea mays), 3'ss of exon 2
aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaacttttatttggaatcataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
|||| | || || ||| || | | | | |||| ||| || | | | | | || | | | ||||||| || ||||| || | |||||||||||||| |||||||||||||| ||||| ||| ||| || | | | || || || | || || || ||||| ||| |
--gtttttccttttttttgtacttttattattcagatcagttgtgaataagtaacctgatcaagt-tcagtcatgctgactgctttgtctt-tatcttagTGGCTGTATAACATCAGCAGAGACGGTTATGCTGGAGAAACAAAGCTTGAGTGACTTCATTGATCACATAAACTCTGATAAAGCTGTTATTGTATCTGTG
upper sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaactttta--tttggaatc--ataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
|| | | | | || | |||| ||| || ||| ||| || | || ||||| | | | | || |||||||||| |||||||||| |||||||||||||| ||||||||||| || || |||||||| | ||| ||| |||| |||| ||||||| ||
---------------------------gtttgtcctctcatttactttgtctgagt-cagttttagagtttagagtgtaatggtttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
upper sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0508g00020.t01 (Vitis vinifera), 3'ss of exon 2
----aaattttacat-tgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaacttttatttggaatcataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
||||||| | ||| ||| |||| | | | || ||| | || | || | || || | || | | | | ||||||||||||| | |||||||| ||||| || ||||| |||||||||||| ||||||||||||| |||||||| ||| ||||| || ||||| || |||
tctaaaattttggttatgaaaagatttgttaaaggtg-gcttttcttgggtaagttatagcaatatggacatc----atagaatttaacctttttaacgatgcagTGGATGCATAACATCAGCTGAGACTGTGATGCTTGAGAAGCAAAGTATGGATGAGTTTCTCTTTAATATTAACAAAGGGAAGGCAGTCATTGTCTCCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgtcaaagtgcaacttttatttggaatcataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
aacttttatttggaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattttacattgattgtgtttcttaagtctatggtgttgttgataatgtcaaagtgcaacttttatttggaatcataatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
- - - - - - gattgtg
- - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -agtgcaa