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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgggcagataatgaatttgcgtgatcatttgctggttctgcacatgatgcactgaacatggagttctgtgttatctaaatgtattctattgtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA

Basic information

species Oryza sativa
transcript LOC_Os07g14270.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 1
cgggcagataatgaat-ttgcgtgatcatttgctggttctgcacatgatgcactgaacatggagttctgtgttatctaaatgtattctattgtg-tgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA
      |||    |||  ||  ||    |||  | || |  |  |  ||    | |   ||   ||     | ||   | | |   || ||||| ||  ||||||| ||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||| || || || |||||||||||| | ||
--ataggatctccaatactgactgtcagttttgttgtaccacgaagcattttgtaattttgacattacccttcatgacattttgcactgttgtgatggccagATGGCTGGGAAAGTCGGTGGGTCAAGTCCGAGTGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACCTCGGGAAAATGGAATGGAGATGCCGA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 1
cgggcagataatgaatttgcgtgatcatttgctggttctgcacatgatgcactgaacatggagttctgtgttatc--------taaatgtattctattgtg-tgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA
         |  | || | |   |   | ||   ||| || | |    | |          |  | | | ||| |         |  | |   || ||||| ||  ||||||| ||||||||||||||||||||||| || ||||| ||||| || |||||||||||||||||||||||||| || ||||| |||||||||||| | ||
---------ataggatctccaatactgtctgtcagttttgtataccgcgaaacattttctaatgtttatattaccatctgtgacatttctgcgctgttgtgatggccagATGGCTGGGAAAGTCGGTGGGTCAAGTCCGAGTGGAAAAAGGACGATAACATGGCTGGTGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 1
cgggcagataatgaatttgcgtgat-catttgc-tggttctgcacatgatgcactgaacat-----ggagttctgtgttatctaaatgtattctattgtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA
      | || |   ||| |||| | ||| ||  |  || |    |   |  | | |  ||         ||||   |  | |  ||||  | | | |||    |||| ||||||| || ||| ||||| || ||||| ||||| || ||||||||| ||||||| || ||||||||||| |||||  | |||||||||||  || |
------ggtagtcccttttcgtggttcatctgtatctttttttttaatcttaaatcagtattttccatttttctaactcgtgtgcatgtgctttgt-gtgaatgcagACGGATGGGGAAATCGTTGGGTTAAATCAGATTGGAAAAAAGATGAGAACCTGGCTGGGGAGTGGAACCACACCTCTGGCCAATGGAATGGAGACGCTAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 1
cgggcagataatgaatttgcgtgat-catttgctggttctgca---catgatgcactgaacatggagttctgtgttatctaaatgtattctat-tgtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA
    | | || |   ||| ||   | ||||||    ||||  |   |  |||        |      ||||   |  | |  ||||  | | | ||  ||| |||| || ||||||| ||| ||||| || ||||| ||||| || ||||||||| ||||||| || ||||||||||| |||||  | |||||||||||  || |
----cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctttgtgtggatgc-cagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 1
cgggcagataatgaatttgcgtgatcatttgctggttctgcacatgatgcactg-aacatg---gagttctgtgttatcta-aatgtattctattgtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA
    | ||||||  ||    ||  ||| ||  |   || | |  || |    |   || |    |  ||  || | || |  |||  ||| |    |      |||||||||||| | |  |||||| || || ||||||||||| ||||||||||||||||| ||||||||| |||| ||||| || ||| ||||||| ||  |
----ctgataatccatgcttgtt-tcaattaataaatcagtatttgctttcttatgactttcctgcattgggtctaatatgtaattcatttttgaatactttaagATGGATGGGAGAATAAGTGGGTTAAATCCGAATGGAAGAAAGATGAGAACATGGCTGGGGAATGGAACTACACCTCTGGTAAATGGCATGGAGACCCGAA

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|29675378|gb|CB671653.1|CB671653
EST:     GCCGCTGTCGCCGGCCAGGTCTTCTTCCAGGAGAAGTTCGAAG                         ATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGACAACA
genomic: GCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
EST: gi|6012783|gb|AU078600.1|AU078600
EST:     CGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAG                         ATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
genomic: CGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     GCCGCTGTCGCCGGCCAGGTCTTCTTCCAGGAGAAGTTCGAAG                         ATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
genomic: GCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
EST: gi|88312709|gb|CI587617.1|CI587617
EST:     GTCCGTCGCCGCTGTCGCCGGCGATGTCTTCTTCCAGGAGAAGTTCGAAG                         ATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAAAA
genomic: GTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
EST: gi|88311943|gb|CI577549.1|CI577549
EST:     GTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAG                         ATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
genomic: GTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
EST: gi|58604287|gb|CK014815.1|CK014815
EST:     GTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAG                         ATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
genomic: GTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
EST: gi|88348476|gb|CI629965.1|CI629965
EST:     GTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAG                         ATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA
genomic: GTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACA

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: 64 (upstream exon), 75 (downstream exon)
Score: 125

AGGTCCTCCTCCTACGCCGCCGCGGCGGTCGCGCTGGCGCTCGCGCTGGCGTCCGTCGCCGCTGTCGCCGGCGAGGTCTTCTTCCAGGAGAAGTTCGAAGgtgaatggct ... gtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcactgaacatggagttctgtgttatctaaatgtattctattgtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA
                           atctaaa  putative branch site (score: 125)
                         ttatctaaatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgggcagataatgaatttgcgtgatcatttgctggttctgcacatgatgcactgaacatggagttctgtgttatctaaatgtattctattgtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - ttgcgtg
- - - - - - - - - - - - - -tttgctg
- - - - - - - - - - - - - - - - - -ttctgca
- - - - - - - - - - - - - - - - - - - - - - tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtta