Sequence
atgc intronic sequence ATGC exonic sequence...agaactgcatttatgttttgtgcatttaatgtctcttcttttatttggttttgatgttttcacctaattgggcttttgatttgacttgatcatgttgcagGTTGAGTCGGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA10G24620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G24620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G356938_T01 (Zea mays), 3'ss of exon 1
agaactg--catttatgttttgtgc-atttaatgtctcttcttttatttggttttgatgttttcacctaattgggcttttgatttgacttgatcatgttgcagGTTGAGTCGGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
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aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagtttttattacaagaactaatagc---acactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG
upper sequence: GLYMA10G24620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G04690.1 (Arabidopsis thaliana), 3'ss of exon 2
---------agaactgcatttatgttttgtgca-tttaatgtct----cttcttttatttggttttga--tgttttcacctaat----tgggcttttgatttgacttgatcatgttgcagGTTGAGTCGGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
||| ||| | ||| | | ||| |||| | ||| | || | || || | |||| | || | || | || || | || |||||||| | |||||||||||||||||||||||| |||| | ||| |||||||| ||||| || ||||| ||||| ||||||||||| ||||| || || |
gtttgtaatctgactctctttttctttaatttactttcatgtttgcgtcttatcttgtacagtcttaagttgttgtagtctcgtgttatgtagctcaagttatgctcttctgttatgtagGTTGAGACAGAGTTTCTTCCTCTGTACACCAACCATGGTATAGGTCTCACTACCTGGAGCCCACTTGCATCTGGTGTGCTCACTGGTAAATACAACAAGG
upper sequence: GLYMA10G24620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0051g00650.t01 (Vitis vinifera), 3'ss of exon 1
-agaactgcatttatgttttgtgcatttaatgtctcttcttt--tatttggttttgatgttttcacctaattgggcttttgatttgacttgatcatgttgcagGTTGAGTCGGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
| ||| | | | |||| ||| || | | | | | | || | | | | || || || ||| | | || ||||| |||| |||| |||||||| |||| ||||||||||| ||| || || ||||||||||| ||||| || |||||||| ||||| ||||| || || |
tatggctg-acaagaactacattgatttgttgtttcatataggatgtataatgttaaaatcctttac--atacggtttctgacatttttctatataaactcagGTCGAGTGTGAGTACCTTCCTCTATACAGCAACTATGGCATAGGTCTTACCACATGGAGTCCACTTGCATCAGGAGTGCTTACTGGAAAATACAACAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttttgatgttttcacctaattgggcttttgatttgacttgatcatgttgcagGTTGAGTCGGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
ttttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaactgcatttatgttttgtgcatttaatgtctcttcttttatttggttttgatgttttcacctaattgggcttttgatttgacttgatcatgttgcagGTTGAGTCGGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -tgcattt
- - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg