Sequence
atgc intronic sequence ATGC exonic sequence...ttttaatgtaggtgtcacattgtcaattgataaatcatttatgtacatggtgcagtaaatatcttgataaaatttattaatggtgcaattttctctgcagAATGATTTGAAGGAACTGTGGTCGCTTTTAAATTTACTTCTTCCAGAGGTTTTTGACAATAAGAAAGCCTTTAACGATTGGTTTTCAAAGCCATTTCAAA
Basic information
species | Glycine max |
transcript | GLYMA18G46930.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 9
ttttaatgtaggtgtcacattgtcaattgataaatca---tttatgtaca-tggtgcagtaaatatcttgataaaatttattaatggtgcaattttc--tctgcagAATGATTTGAAGGAACTGTGGTCGCTTTTAAATTTACTTCTTCCAGAGGTTTTTGACAATAAGAAAGCCTTTAACGATTGGTTTTCAAAGCCATTTCAAA
|||| | | || | | || || | ||| ||| | | | |||| | | |||| | | ||||| ||||| | |||||||||| |||| ||||| ||||||||| ||||| | |||||||| || || ||||||||| ||||| ||| | ||||||||||| || || |||||||
------cataggaatagaactggctactggaaattttcattttttgtgctctatttcagtttgttttttgagttgaggttaaaatggactgatttttcttttgcagAATGACCTGAAAGAACTCTGGTCGCTTCTAAATCTGCTTCTTCCTGAAGTGTTTGACAATCGAAAAGCTTTTCATGATTGGTTTTCGAAACCTTTTCAAA
upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ33371 (Selaginella moellendorffii), 3'ss of exon 5
ttttaatgtaggtgtcacattgtcaattgataaatcatttatgtacatggtgcagtaaatatcttgataaaatttattaatggtgcaattttctctgcagAATGATTTGAAGGAACTGTGGTCGCTTTTAAATTTACTTCTTCCAGAGGTTTTTGACAATAAGAAAGCCTTTAACGATTGGTTTTCAAAGCCATTTCAAA
| | | ||| | || | |||||| ||| | | ||| || | || ||||| ||| | | || |||||||| ||||||||| |||| ||||| || || |||||||| | ||||| ||| |||| ||||| ||||||||||| ||||
----------------------------gtaagagtattggcttttatactatc-taaata-cttaagttatttttttggttgtatgt---------cagAACGATCTACATGAGCTGTGGTCACTTTTAAATCTACTCCTTCCTGAAGTCTTTGACAACAGTAAAGCTTTTCACGACTGGTTCTCAAAGCCATTCCAAA
upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ30636 (Selaginella moellendorffii), 3'ss of exon 5
ttttaatgtaggtgtcacattgtcaattgataaatcatttatgtacatggtgcagtaaatatcttgataaaatttattaatggtgcaattttctctgcagAATGATTTGAAGGAACTGTGGTCGCTTTTAAATTTACTTCTTCCAGAGGTTTTTGACAATAAGAAAGCCTTTAACGATTGGTTTTCAAAGCCATTTCAAA
| | | ||| | | || | |||||| ||| | | ||| || | || ||||| ||| | | || |||||||||||||||||| |||| ||||| || || |||||||| | ||||| ||| |||| ||||| ||||||||||| ||||
----------------------------gtaagagtattggtttttatactatc-taaata-cttaagttatttttttggttgtatgt---------cagAACGATCTACATGAGCTGTGGTCGCTTTTAAATCTACTCCTTCCTGAAGTCTTTGACAACAGTAAAGCTTTTCACGACTGGTTCTCAAAGCCATTCCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catggtgcagtaaatatcttgataaaatttattaatggtgcaattttctctgcagAATGATTTGAAGGAACTGTGGTCGCTTTTAAATTTACTTCTTCCAGAGGTTTTTGACAATAAGAAAGCCTTTAACGATTGGTTTTCAAAGCCATTTCAAA
tattaat putative branch site (score: 2)
ttttctctgc putative PPT
agtaaatatcttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttaatgtaggtgtcacattgtcaattgataaatcatttatgtacatggtgcagtaaatatcttgataaaatttattaatggtgcaattttctctgcagAATGATTTGAAGGAACTGTGGTCGCTTTTAAATTTACTTCTTCCAGAGGTTTTTGACAATAAGAAAGCCTTTAACGATTGGTTTTCAAAGCCATTTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - aatgtag
- - - - - - tgtcaca
- - - - - - - - - - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - - - - - - -tggtgca