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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagttgttttgtcattttctttcaagttaattgaagaggctccttgattttttttccatactatgaaaatattaatgtctactggtgatttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGATGCCTTGACTGTGGATACGGCTTTTAGTTGTGCACGAGGGCTTCCTCCAG

Basic information

species Oryza sativa
transcript LOC_Os04g37660.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G015610_T02 (Zea mays), 3'ss of exon 5
--ttttag----ttgttttgtcattttctttcaagttaattgaagaggctccttgattttttttccatactatgaaaatattaatgtctactggtgatttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGATGCCTTGACTGTGGATACGGCTTTTAGTTGTGCACGAGGGCTTCCTCCAG
  | | ||     | || ||| ||||||| | ||||  |||       |   || || |  |   |||| | ||||||   |||||     | |  ||   |  |||| || |  ||||||||  |  | |||||||||||||| |||||||||||||| ||||||| ||| | ||||||||| |||||||| ||||||||||| |
tttctgagaggactattctgtgattttctctgaagt-gattctttgttcattttaatctgat---catattttgaaaaa--taatgctgtattgcaatgcttgtagCTGTCTAACGCTGGAGGTCGTCTTATTATTTCAAGTGACGGTGTTTGGGATGCTTTGACTGCGGAAATGGCTTTTAGATGTGCACGGGGGCTTCCTCCTG

upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 5
---ttttag----ttgttttgtcattttctttcaagttaattgaagaggctccttgattttttttccatactatgaaaatattaatgtctactggtgatttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGATGCCTTGACTGTGGATACGGCTTTTAGTTGTGCACGAGGGCTTCCTCCAG
   | | ||    || |  ||| ||||||| |  ||| | |       | || || |  |    || | | | ||||||    |||||    | |  ||   |  |||| || | |||||||||| |  | ||||||||||| || |||||||||||||| |||||||  || | ||||||||  |||||||||||||||||||| |
ttttctgagaggattatcctgtgattttctctggagtgattctt---tgttcatttaaatcggatcgaaatt-tgaaaa---caatgttgtattgcaatgcttgtagCTGTCTAATGCTGGAGGCCGTCTTATTATTTCAAGCGACGGTGTTTGGGATGCTTTGACTGCAGAAATGGCTTTTAAATGTGCACGAGGGCTTCCTCCTG
















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|29636845|gb|CB641854.1|CB641854
EST:     AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAG                         CTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
genomic: AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
EST: gi|88372968|gb|CI640419.1|CI640419
EST:     AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAG                         CTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
genomic: AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
EST: gi|88333501|gb|CI656573.1|CI656573
EST:     AGGATGTACGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAG                         CTATCAAGTGCTGGAGGCAGAATCATCATTTCAAGTGATGGTGTTTGGGAT
genomic: AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
EST: gi|40490361|gb|BX899888.1|BX899888
EST:     AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAG                         CTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTATGGGAT
genomic: AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
EST: gi|27547836|gb|CA765984.2|CA765984
EST:     AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAG                         CTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
genomic: AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
EST: gi|88296263|gb|CI667653.1|CI667653
EST:     AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAG                         CTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
genomic: AGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
EST: gi|58605846|gb|CK033879.1|CK033879
EST:     GGATGTAGTGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAG                         CTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT
genomic: GGATGTAG-GTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGAT

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: 72 (upstream exon), 65 (downstream exon)
Score: 16

ACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGCAGATCAAGgtattattaa ... atttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGATGCCTTGACTGTGGATACGGCTTTTAGTTGTGCACGAGGGCTTCCTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgattttttttccatactatgaaaatattaatgtctactggtgatttcttcagCTATCAAGTGCTGGAGGCAGAATCATTATTTCAAGTGATGGTGTTTGGGATGCCTTGACTGTGGATACGGCTTTTAGTTGTGCACGAGGGCTTCCTCCAG
                           tattaat  putative branch site (score: 16)
                                              tttcttc  putative PPT
     ttttttttccatacta  TA-rich tract