Sequence
atgc intronic sequence ATGC exonic sequencegtaactatggtatttcgtttatgatggtatttatgtaggattattcccaaattattcttacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g29050.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
gtaactatggtatttcgtttatga-tggtatttatgtaggattattcc-caaattattcttacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
|||||| ||| | | || || || ||| |||| | | | | || || ||||| ||| |||||||||| || ||||||||||||||||| |||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||
---------gtattttgttgttatcttctacccattcagatgtatggggcaaagtccctaaatgtcacttcatct-ctgtaaata-gGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 10
----------gtaactatggtatttcgtttatgatggtatttatgtaggattattcccaaattattct-------tacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
|| || | ||| || || || || ||| || || || | | ||| || || | | | | || |||||||| |||||||| ||||| || |||||||||||||| | || || ||||||||||| |||||||||||||||||||| ||||| || |
cactttgaatgtg-ttaagatatgtcattcattatta-attgatcatagactagctctttcctgttcaacgatagtaatagattcattttcaattttgacagAGAATCTGAACCAAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
-------gtaactatggta---tttcgtttatgatgg--tatttatgtaggattattcccaaattattcttacctgagttttcctgctgtacata---agGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
| | | || || | || || || || || | || | | || || | | ||| | ||| | | | | || |||||||| || ||||| ||||| || |||||||||||||| | || || ||||||||||| |||||||||||||||||||| ||||| || |
ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 11
--------gtaactatggta----tttcgtttatgatggtatttatgtaggattattcccaaattattcttacctgagtttt---cctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
|| | || | ||| | || || | | || || | | || | ||| | | || | || || || ||||||||||||||||| ||||| ||||| ||||||||||| |||| || | ||| ||||| || ||||| ||||| ||||| || |||||||| |
cattacaattagccgtgttggagccttcactattgctgatgagtctgcttttctaagttcttagtaatattatataatttgtaattttgttggttgatagAGAATCTGAGCCAAATTCATGGGAAGACACCATGAAAGATGAATTGGATCGCAAGAAGTATCCCCGTATGCCATGGCACGATGTCCATTGTGCTCTTTGG
upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtaactatggtatttcgtttatgatggtatt-tatgtaggattattcccaaattattc----ttacctgagttttcctg----ctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
| || || || | | ||| | | ||| | || | || | | | || || | | || | || | | | ||||||||||| |||||||| ||||| || |||||||||||||| |||| || ||||||||||| ||||| |||||||| || || ||||| || |
gtgtgagaacattgacaatagtttcttcttttctaagtaattgcaagtttgttttcactctggctctttcacattggataacttgtaatgaattttcaatttcagGGAATCTGAACCAAATTCTTGGGAAGATACAATGAAAGATGAATTGGATCGTGGAAAATATCCTCGTATGCCATGGCATGACGTCCATTGTGCCCTATGGMapped 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|58669537|gb|CK058223.1|CK058223EST: TCAGATGTTCCTCCTGTGATATGGCCA-GGAAAGACTACTATAACCCCAG GGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCG
genomic: TCAGATGTTCCTCCTGTGATATGGCCAGGGAAAGACTACTATAACCCCAGgtaactatgg ... tgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCG
EST:
gi|58692366|gb|CK081053.1|CK081053EST: TCAGATGTTCCTCCTGTGATATGGCCAGGGAAAGACTACTATAACCCCAG GGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAG
genomic: TCAGATGTTCCTCCTGTGATATGGCCAGGGAAAGACTACTATAACCCCAGgtaactatgg ... tgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAG
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:
66 (upstream exon),
27 (downstream exon)
Score:
5GAGGTCTTGATCTGTGCTTTGGTCGCTACGATAATTCTGCGCACAAACTTTCAGATGTTCCTCCTGTGATATGGCCAGGGAAAGACTACTATAACCCCAGgtaactatgg ... tgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtaggattattcccaaattattcttacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
ttcttac putative branch site (score: 5)
ttttcctgct putative PPT
aaattattctta TA-rich tract