Sequence
atgc intronic sequence ATGC exonic sequencegtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g28180.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
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---------------------------------------------------aggcaacaccaccagcaaatggcataac------------cttttgcacttcagtttcttt-------attttgaaagatgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
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------------------------------------------------------------------------gtatgacccttttttcaattgattac--------ttggttgtgaga---tttgtagtttgctaattttagttgaa--tgtt--------ttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 16
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
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----------------------------------------------------------------------------------------------gtatggcccttttttcaattgattacttggttgtgatatttgtagttgctaattttagtttattt--ttttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
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------------------------------------------------------------------------------------------gtttgtggagactg-cctgcatgtattacatatgt------attattgtttctgttctaagaagacatttcttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatct--aattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
|||||||| || | | | ||| | | || ||| || | | | | | | | | || | ||| | | |||| || | ||||||||||||| ||||| || | |||||||| ||||||||| | || || || ||||||||||| || |||||||||| || ||||| ||||||||||
-----------------------------------------------------------------gtaaaaagggagatgatgctgttttgaatatatctacactgacttgattattccatagtatctgattggctgtgattgcat------gttggttac---------agATTGGTCTGGCTATGTCTCCTCTGAGCAACAATTCCTTGTTTTTGGACTATCATCGGAATCCTTTTCCTATGTTTTTCCTTCGGGGCCTCAATGTTTCCC
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 15
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
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---------------------gtgtggcactcttcctctaagattat-tgcttgatctttactctccgtctctcagatgagatccatcatat-agggtgacataaccgggt----gaaagatatatctatcacga----ctcatatgtttctcattatcgattta--cagATTGGATTGGCCATGTCTCCTTTAAGCAACAACTCCCTTTTCCTAGACTACCATCGCAATCCTTTCCCCATGTTCTTTTCTCGAGGTCTCAACGTATCGTMapped 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|33796571|gb|CF324153.1|CF324153EST: TCAACTTAAGGAAATCTCCTGTGCTTCAATATCTATACTATCTTGGCCAG ATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC
genomic: TCAACTTAAGGAAATCTCCTGTGCTTCAATATCTATACTATCTTGGCCAGgtaattcttc ... attttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC
EST:
gi|27548799|gb|CA767547.2|CA767547EST: TCAACTTAAGGAAATCTCCCGTGCTTCAATATCTATACTATCTTGGCCAG ATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC
genomic: TCAACTTAAGGAAATCTCCTGTGCTTCAATATCTATACTATCTTGGCCAGgtaattcttc ... attttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTAC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
73 (upstream exon),
68 (downstream exon)
Score:
13CGATCACTTGGCAGCAACATTTCTTCTTTGTCACAATATATCGCATGGAATCAACTTAAGGAAATCTCCTGTGCTTCAATATCTATACTATCTTGGCCAGgtaattcttc ... attttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
ttttatc CT-rich tract
tttcaattttatca TA-rich tract