Sequence
atgc intronic sequence ATGC exonic sequence...cattacattgtcttatttcttttgttcttgtcacttttatgctgtcaatttttcaacattggttgttgtattttctctcattaaaataacctattgatagGTTATTAGGAGTGTGAGTCAATGGTCTGCTGGAACAAGTCAAACCGAAGAGAGCATCCACAATGCTTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
Basic information
species | Glycine max |
transcript | GLYMA09G04620.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 11
-------cattacattgtcttatttcttttgttcttgtcacttttatgctgtcaatttttcaacattggttgttgtattttctctcattaaaataacctattgat--agGTTATTAGGAGTGTGAGTCAATGGTCTGCTGGAACAAGTCAAACCGAAGAGAGCATCCACAATGCTTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
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gatatgcttgtatactaaattactaaactaacattagaaaccattataata--attgcatcaaa--taattctagtaagtt-----aatgaatttatattttggttcagGTAATTAGAAGTGTTGGTCAATGGTCAGCTGGAACCACTCAAATCGAAGGAAGCATCCACAATGCCTATTTTTCTCTTATTGAAAAGGCAGAACATTTTG
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 11
cattacattgtcttatttcttttgttcttgtcacttttatgctgtcaatttttcaacattggtt-gttgtattttctctcattaaaataacctattgat-agGTTATTAGGAGTGTGAGTCAATGGTCTGCTGGAACAAGTCAAACCGAAGAGAGCATCCACAATGCTTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
| |||| || |||| | | || ||| ||| ||| |||||| || ||| | | | | | | | | | | ||||| |||||||||| |||||||||| ||||| || | ||||| |||| |||||||||||||| || | ||||| |||||||| || ||| |||||
-aagacatgcctgtacgcttttttcacctcgaacggacatg-tgtatttttgcatacattgttttattgaagtattttatgaatgtgtgatttttcgctcagGTTGTTAGGAGTGTCGGTCAATGGTCAGCTGGGACCACTCAAATTGAAGGAAGCATCCACAATGCCTACTTTTCTCTGATTGAGAAGGCAGAACACTTCG
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 13
-cattacat-tgtcttatttcttttgttcttgtcactttta-tgctgtcaatttttcaacattggttgttgtattttctctcattaaaataacctattgatagGTTATTAGGAGTGTGAGTCAATGGTCTGCTGGAACAAGTCAAACCGAAGAGAGCATCCACAATGCTTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
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aatttatatatgttgtcactctagcatatttatgggattgaatccttttttcattataatattatttgtttaactatcagaaat---aatatctcactttcagGTTATTAGGAGCGTCAGTCAGTGGTCTGCTGGAACAAGCCAAGTTGAAGACAGCACTCATAATGCTTATTGCTCCCTTATAGAAAAGGCAGAACACTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatttttcaacattggttgttgtattttctctcattaaaataacctattgatagGTTATTAGGAGTGTGAGTCAATGGTCTGCTGGAACAAGTCAAACCGAAGAGAGCATCCACAATGCTTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
aaataac putative branch site (score: 2)
tattttctctcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattacattgtcttatttcttttgttcttgtcacttttatgctgtcaatttttcaacattggttgttgtattttctctcattaaaataacctattgatagGTTATTAGGAGTGTGAGTCAATGGTCTGCTGGAACAAGTCAAACCGAAGAGAGCATCCACAATGCTTATTGCTCTCTTATTGAGAAAGCTGAATACTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - tgtcact
- - - - - - - - - - - - - - - - - - - -tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa