Sequence
atgc intronic sequence ATGC exonic sequence...ttctgcagaagaaaaattgttcaagtgtgaaaagaaaccaatgcacaattttgtcaatggaatcgttaacaattttcttttgttgcttttttatatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
Basic information
species | Glycine max |
transcript | GLYMA12G35840.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 3
--ttctgcagaagaaaaattgttcaagtgtgaaaag----aaaccaatg-cacaattttgtcaatggaatcgttaa--caatttt---cttttgttgcttttttata--tgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
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gtacttgttgcaaacattatgttcatttacaaaatgctttgcattattttcagcatgaggtcagaaagatccataatccattcttatgcttcacctgacatcctattattttagATCCAAGCTGCCTTTAGAACCGATGAGATCCGAAGAACACAGCCCACTCCCCAAGATGAAATGCGTGCTGGCATGAGCTACTTCCATGAAACAATATGGA
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 3
------------------ttctgcagaagaaaaattgttcaagtgtga----aaagaaaccaatgcacaattttgtcaatggaatcgttaacaattttcttttgttgcttttttatatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
|| | |||| | || ||| ||| ||||| | ||| | ||||| | | |||| || | ||||| |||||| | |||| ||||||||||| | || ||||| ||| | || || | || || || |||||||| ||| | || || |||||||||||||| |||||||||||||
gtacttctttcaatctaattttattacctaaaattctttgaagcttgagaccaaagagattaattcttaatttc-ttacctgaat-----acctctctcttt-----ctttttca-----agATCCAAGCTGCCTTTAGAACTGATGAGATCCGAAGAACACAGCCCACTCCCCAAGATGAAATGCGTGCTGGTATGAGCTACTTCCACGAAACAATTTGGA
upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 3
ttctgcagaagaaaaattgttcaagtgtgaaaagaa-accaatgcac--aattttgtc---aatggaatcgttaac---aattttcttttgttgcttttttatatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
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---------aattgctctatttgagttacaaatgaagattgttgtttggaggcttgcccgaaatacgaccgtttttctgaattaccattttctgttatttttcctgcagATTCAAGCAGCATTTCGCACAGATGAGATCCGGAGGACCCCTCCTACTCCACAAGATGAGATGAGGGCAGGAATGAGTTATTTCCATGAAACAATCTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattttgtcaatggaatcgttaacaattttcttttgttgcttttttatatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
cgttaac putative branch site (score: 3)
ttttcttttgttgctt putative PPT
ttaacaattttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctgcagaagaaaaattgttcaagtgtgaaaagaaaccaatgcacaattttgtcaatggaatcgttaacaattttcttttgttgcttttttatatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
ttctgca
- - - - aagaaaa
- - - - - - - - - - - aagtgtg
- - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - -aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - caatgga