Sequence
atgc intronic sequence ATGC exonic sequencegtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
Basic information
species | Glycine max |
transcript | GLYMA13G00980.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 10
gtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattga--aatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA--------------------
| | || | ||| || | ||| | | | |||| |||| | | |||| ||| || ||| ||| | |||||||| ||||||| |||||||| || || || ||||| ||| |||||||||| |||||||||||||| || ||||| |
-----------------------------------------------aactttcatcattga-ttcactgtgctc--ctttcaactttgaaaaaacaaattactatgcaggcccgaatgacacaacttcaagatgcccaaaagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 11
--gtaattacttattagtatcactttcc--aatttttatcttttaagtatttgcatatatgaatgaa---ttgattgtctttggttgttaactgcttgaaaattgaaat----atgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
||| ||| | || | ||| || | | || || | | |||| | | | |||||| || || | || ||||||| |||| ||| ||| || ||| ||| | |||||||| ||||||| |||||||| || || || ||||| ||| |||||||||| |||||||||||||| || ||||| |
gtagaatgactgaataagacaactcacctgacccctcatggttgatgctccagcatgcaaactttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G147500_T02 (Zea mays), 3'ss of exon 11
---gtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
| | ||| | | | | || | | | || | | |||| | || || ||| | | || ||| | || | | | ||| || ||| ||| | ||||||||||| || | |||||||| ||||||||||| ||||| |||| |||||||||||||||||||| || |||||||
gtaggagccactggattgagactataagcatcgtacaattgctatttctcc-catacacacttgttttcattacat---gatgataattatttctgat----gacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCTGAGGCAACTGACCGGGAGCTTGAGCTTGAAGCTCAACTGGTTGAAGCAA
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 12
gtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
|| | | | | |||||||||| || | | ||| || | || | | |||| | || | || || | | |||||||||||||||||||| |||||||| || || | ||||| ||||||||||| || ||||||||||| ||||||||||||||||||||||| || |||
------gtaggttgtttttttctacatatttttatctcatat-ttcctattgataacaaaacctagactttttttg--taatatttatttttctgctgtatttgaaagGAGCGCATGGTTCAATTACAAGATGCACAGAAAGGGGCAGAGGTTACTTCTGAAGCAACTGAGAGGGAGCTTGAGCTTGAAGCTCAACTTGTTGAGGCACMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|10236681|gb|BE805569.1|BE805569EST: CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG GAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT
genomic: CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattactt ... aaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT
EST:
gi|51344846|gb|CO985579.1|CO985579EST: CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG GAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT
genomic: CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattactt ... aaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
tgttaac putative branch site (score: 2)
ttgaaaattgaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA