Sequence
atgc intronic sequence ATGC exonic sequence...ttgggggtggagtggagtggggctggtacggttggttatatgtaatctactgtcactatcatctcatctcttaactctttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATCGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA
Basic information
species | Glycine max |
transcript | GLYMA15G07760.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 12
ttgggggtggagtggagtggggctggtacggttggtt-atatgtaatctactgtcactatcatctcatctcttaactct---ttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATCGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA------------
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-------------------gtgctaccataattctttgatgccttacttagtttttctttc--ccaaataaagaactatgtattgatgtttgttttgctgatagCACTCCAACTGGTGTGGAAACACCTGATGTGATTGATCTTCGGAAGCTGCAGCGGAAAGAGCCTGAAAAGCAGACCGAGAAGCAACTATACCAG
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G132060_T02 (Zea mays), 3'ss of exon 11
--------------ttgggggtggagtggagtg-gggctggtacggttggttatatgtaatc-tactgtcactatcatctcatct-cttaactctttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATCGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA------------
|| | ||| || || | | || | | || | | ||| | | | | | | ||||| ||| || | || | ||| ||||| ||||| || ||||||||||||||||||||||| ||||||| |||||||||||| |||| | || | |
gtggtttactatatttctttctttagtattttgtaggtccttgttttcccttttctttagtaatgctgatgcagtagacatgtatgcctaacttttttttac----ctccaac-cagTACTCCAACTGGTGTTGAAACACCTGATGTTATCGACCTTCGGAAGCTGCAGAGGAAGGAGACTGACAAGCAGGCAGAACGGCCGCTGTACCAG
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 7
---------------ttgggggtggagtggagtggggctggtacggttggttatatgtaatctactgtcactatcatctcatctcttaactctttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATCGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA------------
| | | | | | | |||| | | | ||||| || | | | | | ||| ||| || ||| | || | ||| ||||| ||||| || ||||||||||||||||||||||| ||||||| |||||||||||| |||| | || | |
gtgatttacgtatttctctgtattgttttgtaggcacttggttttccttttctttagtaat--ggtgatgcagtacacatgtagcctaattctctctc-tgcgtc--caac-cagTACTCCGACTGGTGTTGAAACACCTGATGTTATCGACCTTCGGAAGCTGCAGAGGAAGGAGACTGACAAGCAGGCAGAACGGCCGTTGTATCAG
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 4
ttgggggtggagtggagtggggctgg-tacggttggttatatgtaatctactgtcact-atcatctcatctcttaactctttcctatgcattttcac-ctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATCGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA
||| | | | | |||| | | | | || | |||| | ||| | |||| | | | || | | | | || ||||||| || ||||| || || |||||||||||||| ||||| || |||||||||||||||||||| |||||||| |||||||||
---gggaccattagtaaggagtctgggcaagtctttctgcatatcatcttaagaaacttgtaatctttattaatgatcactttttttccctcctcttattcagCACCCCAACTGGTGTTGAGACACCTGATGTTATTGACCTACGTAAGCAACAGAGGAAGGAGCCAGAGAGGCCACTTTATCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctactgtcactatcatctcatctcttaactctttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATCGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA
tcttaac putative branch site (score: 2)
ttttcacctc putative PPT
attttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgggggtggagtggagtggggctggtacggttggttatatgtaatctactgtcactatcatctcatctcttaactctttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATCGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - gggtgga
- - - - - - - gagtggg
- - - - - - - - - - -gctggta
- - - - - - - - - - - - - - - gttggtt
- - - - - - - - - - - - - - - - - - - - - - - - -ctgtcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcatt