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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataaaatacaaacatatattatatatgctagcagtatgttgtacagttgattcacatcaagctgtagttgactatggtgtatcttgtcattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G060977_T01 (Zea mays), 3'ss of exon 5
gtaaataaaatacaaa----catatattatatatgctagca---gtatgttgtacagttgattcacatcaagctgta--------------gttgactatggtgtatcttgtcattga-atagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG
|||||||| |||||||     |  | || | | || ||       |||  |||||  | |||     || || | ||               |||| |||||||||  ||    || | | ||||||||||||||||||| |||||||| || ||||| || ||||| ||||||||||||||||| || ||||||||||| |||||||||||
gtaaataacatacaaaaggttaccttttctttctggtaattttcatattgtgtaccatagataagtgtccagatatatttgcctatttggtattgattatggtgtaaatttctcttaacacagGAAGAAATGAAATCACAAGGATCAAAGAAAGCTACAAGGATATTCGTTGCTCGAATTCCGCAATCGGTGGATGAGTCGATGTTTCGTAG

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G030902_T04 (Zea mays), 3'ss of exon 4
gtaaataaaatacaaacatatat----------tatatatgctagcagtatgttgtacagttga---ttcacatcaagctgtagttgactatggtgtatcttgtcattga-atagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG
|||||||| ||||||| |  ||           | ||| | |     || ||    || | | |   | || ||  || ||   |||| |||||||||  ||    || | | ||||||||||||||||||| ||| |||| || ||||| || |||||||||||||||||||| ||||| ||||| ||||| |||||||||||
gtaaataacatacaaaaacttaccttttctttctgtattttcatctggtctgcctcaccgataagtgtccagatgcagttggtattgattatggtgtaattttctcttaacacagGAAGAAATGAAATCACAAGGAACAAAGAAAGCTACAAGGATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG
















Mapped 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|117251528|gb|CT844202.1|CT844202
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|33682634|gb|CF310873.1|CF310873
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|58598133|gb|CK008661.1|CK008661
EST:     GCCACTCCTAAG                         GAAGAAATGAAATCACAGGCATCAAAAAAGGCTACTAGAATATTGGTTGCT
genomic: GCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|58672423|gb|CK061109.1|CK061109
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACT
EST: gi|58676983|gb|CK065670.1|CK065670
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGACATGACATCCCAGGGATCACAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|29677102|gb|CB673377.1|CB673377
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|116875665|gb|EC366173.1|EC366173
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|58676963|gb|CK065650.1|CK065650
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGACATCACAGGGATCAAAAAAGGCTACTAGAATA
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATA
EST: gi|58591906|gb|CF990214.1|CF990214
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|33800393|gb|CF326065.1|CF326065
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|33684319|gb|CF312558.1|CF312558
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
EST: gi|86596647|gb|CI286560.1|CI286560
EST:     AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG                         GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT
genomic: AGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCT

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: 44 (upstream exon), 74 (downstream exon)
Score: 28

AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAGgtaaataaaa ... cattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagttgattcacatcaagctgtagttgactatggtgtatcttgtcattgaatagGAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG
                       agttgac  putative branch site (score: 28)
                                       tcttgtc  putative PPT
                                              attgaata  TA-rich tract