Sequence
atgc intronic sequence ATGC exonic sequence...tctatgattttatcttaaagttatgttaaacatttctgaaaggtaattctagttaacaaagacggatttgtcgttaacaaacatttttttatttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
Basic information
species | Glycine max |
transcript | GLYMA12G05390.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g41850.1 (Oryza sativa), 3'ss of exon 5
--------------------------------tctatgattttatcttaaagttatgttaaaca-tttctgaaaggtaattctagttaacaaagacggatttgtcgttaacaaacatttttt-tatttga-acagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
| | | | | | ||||| | | | ||| || || | || |||| | | || || | | | |||| |||| | ||||||| ||||||||| | ||| |||||||| |||| |||||||||||| |||||||||| ||||||||||| || || || ||||| || |||||||| ||
gtgagcctctagtgtctttttgtaaaatgaacttaacaaacctttactgt-gttatttgatctactttatgtaaatagggtataattaa--atggttgactttctgctgatgccttcttttaatattgggtgcagTTTGTCCAACAACTTTGAAACGGATATGCCGGCATCATGGAATTTCACGATGGCCATCTCGCAAGATAAACAAGGTTAATCGTTCATTAAAGAAGATTCA
upper sequence: GLYMA12G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------tctatgattttatcttaaagttatgttaaa--catttctga-aaggtaattctag---ttaacaaagacggatttgtcgt------------taacaaacatttttttatttga------------acagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
||| | ||| | || | | ||| || | ||| || || | ||| ||| || | | |||| | | ||| |||||||||| ||||||| || || || || |||||||||||||| ||||||||||| ||||| |||||||| || |||||||| || || ||||| || | |||||||| ||
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
upper sequence: GLYMA12G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
----------------------------------------------tctatgat-tttat----cttaaagttatgtta--aacatttctgaaagg--taattctagttaacaaagacggatttgtcgttaacaaacatttttttatttga--acagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
|| || || | || || | ||| | | | ||||| || | || | | | || | | ||| | | | | ||||||| ||||||||| | ||| | |||||||| |||||||||||||| ||||||||||| || |||||||| || || |||||||| |||||||||| |
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
upper sequence: GLYMA12G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G105004_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------tctatgattttatct--taaagttatgttaaacatttctgaaaggtaattctagttaacaaag-acggatttgtc---gttaacaaacatttttttatttgaac------agTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
| | | | | | ||| || | |||| ||| | | ||| | | | ||| | | | | ||| || ||| || |||||| ||||| || | ||| | |||||||| |||||||||||||| |||||||||| || |||||||| || || || ||||| |||||||||||| |
gtgagccctactgtattgttacgaagtctctgttaaatctagatttgctgtgacattcacagtactgattactgaagataatgccatcattgtagaagaatttcttagattaggagattatggaatgaactgcttcttctgacacttgcctataaacaccattgcagTTTGTCCAACGACATTGAAACGAATATGCAGACAACATGGAATTTCCCGATGGCCATCTCGAAAGATAAACAAGGTCAATCGTTCATTGAAGAAGATAGA
upper sequence: GLYMA12G05390.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0094g00020.t01 (Vitis vinifera), 3'ss of exon 4
tctatgattttatcttaaagt-tatgttaaacatt-tctgaaaggtaattctagttaacaaagacggatt-tgtcgttaacaaacatttttttatttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
| | | | ||| || | | | || | || ||| | | | ||| | | | | | | | | | | ||| ||| | |||||||||| || || || ||||| || ||||| |||||||| || ||||||||||| ||||||||||| || || |||||| | || ||| |||||||||
--agtagtcccaacaactagtataaataagatgttatttggaagaagaagttggcaaactgtgtagtctgatattgattttgattttatctttgtttta-cagTTTGCCCCACTACACTCAAAAGAATCTGCAGACAACATGGGATATCAAGATGGCCGTCCCGCAAGATCAACAAGGTGAACAGATCACTGAGGAAGATACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctagttaacaaagacggatttgtcgttaacaaacatttttttatttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
cgttaac putative branch site (score: 3)
tttttttattt putative PPT
ttaacaaacatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatgattttatcttaaagttatgttaaacatttctgaaaggtaattctagttaacaaagacggatttgtcgttaacaaacatttttttatttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - -ctgaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatttg