Sequence
atgc intronic sequence ATGC exonic sequence...ttcagcagttaaatagtatcatcttttgatttttgtctatttaccaaccaagcatgatgagttgacagggtaatgaatttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g67870.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 5
ttcagcagttaa-atagtatcatcttttgatttttgtctatttaccaaccaagcatgatgagttgacagggtaatgaatttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
| | | |||| ||| |||||| ||| || | ||||| ||||| | | ||| | | | | | | | | ||||| |||| || |||||||||||||| ||||| | ||| ||||| |||||||| |||||||||||||| ||||| |||||||| || |||||||||||||||||||
tactgtggttactatatgttcatctcttggccttgttttattt-tttaccaaagaaggccagtaaattgactcgttactcatgtttatcaaactgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA
upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 5
ttcagcagttaaatagtatcatcttttgatttttgtctatttaccaaccaagcatgat--gagttgacagggtaatga-atttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
| || | |||| | |||| ||| |||| |||| | | | | ||| ||| | | | || | | | ||| || |||| || || | |||||||| || ||||||||||| |||||| ||||||||||||| || || || ||||| |||| ||||| ||||| || |
-ccgacattgaaattttggtccattttcattcttgttgatttcctagattgtctttgctagaggcattttaccaattacactagtattaacaccttg--gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------------------------------ttcagcagttaaatagta--tcatcttttgat-----ttttgtctatttaccaaccaagcatgatgagttgacagggtaatga-atttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
|| | | ||| || | ||||| | |||| | ||| || ||| | || | | | | ||||| || ||||||| |||||||| ||||| || || | ||||||||| || ||| ||||||||||||| |||||||| ||||| ||||| ||||||||||| | || |
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattg-gctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 5
ttcagcagttaaatagtatcatcttttgatttttgtctatttaccaaccaagcatgatgag-----ttgacagggtaatgaatttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
| || ||| | | | | | || | || | || || ||| || || | | | ||| | | | | | || |||| || || | |||||||| |||||||| ||||| || || |||||||||||||| || ||||| |||||||| ||||| || ||| || |
----atatttgtata-cacctgttccctgtaatggttgaagtatttttctagaatcatgtagtttttttgtgctttatcatgtatattctggttctctaatacagGTTGGGGTGGATAGAATGCATAAAGACAGCAAGTATGTATTATTCCTGGATGATGATGTCAGGCTGCATCCTGGGACCATTGGGGCCCTCGTTGCTGAGAMapped 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|33795442|gb|CF323591.1|CF323591EST: TTGTAGCTGGGCTCTCAACAACATGTAGCCAGAAAATCCATAATCAGTTA ATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGAT
genomic: TTGTAGCTGGGCTCTCAACAACATGTAGCCAGAAAATCCATAATCAGTTAgtacgtaaat ... attgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGAT
EST:
gi|58658006|gb|CK046686.1|CK046686EST: TTGTAGCTGGGCTCTCAACAACATGTAGCCAGAAAATCCATAATCAGTTA ATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGAT
genomic: TTGTAGCTGGGCTCTCAACAACATGTAGCCAGAAAATCCATAATCAGTTAgtacgtaaat ... attgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccaagcatgatgagttgacagggtaatgaatttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
tactgat putative branch site (score: 2)
taatgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcagcagttaaatagtatcatcttttgatttttgtctatttaccaaccaagcatgatgagttgacagggtaatgaatttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- cagcagt
- - - - - - - - - - -tcttttg
- - - - - - - - - - - - - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - catgatg