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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttcacctcatataatgctcagcaaatccatgcaagaaaaggaattaatatctccaagtaggatgagcagcaacttgcaaggaacagaagtgcagttccactgaaaacagctggtgttttcttttttttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGAGCCAAGAACGCCGGCCAGGCGCAGGAGTTCGCCGGCGCGCTCGGCTGGA

Basic information

species Oryza sativa
transcript LOC_Os07g04990.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 9
gtgcttcacctcatataatgctcagcaaatccatgcaagaaaaggaattaatatctccaagtaggatgagcagcaacttgcaaggaacagaagtgcagttccactgaaaacagctggtgttttctttttt---ttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGAGCCAAGAACGCCGGCCAGGCGCAGGAGTTCGCCGGCGCGCTCGGCTGGA
| | | || | || ||| || || | || || | || | | || | || ||| || | || | || |||| || | ||||||||| || |||||||||||||| ||||| || || |||||||||||||||||||||||||| ||| ||||||| ||||||||||||| || ||||||||||
--------------------------------------gtatggtgctt--cacctacaaa-agcttggg--acatctccggatcaaagacattcgagatgtac-gaacacggttgatcttccctttgttccttcgtttcagGTGTCTCTGAACTGGCTGACCTGCCAGGGGAACGTGGTGCCAATCCCCGGAGCCAAGAATGCCAGCCAGGCCAAGGAGTTCGCCGGTGCACTCGGCTGGA
















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|88459328|gb|CI517006.1|CI517006
EST:     ACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: ACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|88519585|gb|CI447239.1|CI447239
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATNTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|88663321|gb|CI480586.1|CI480586
EST:     GAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATNTGGTGCCAATCCCCGGA
genomic: GAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|86885123|gb|CI315694.1|CI315694
EST:     GATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGCCTAACATTCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: GATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|29686327|gb|CB682602.1|CB682602
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|86892489|gb|CI311960.1|CI311960
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|88505384|gb|CI432890.1|CI432890
EST:     GAACAGGATCAAGGAGATTGGGAGAAAGCTATGGGAAGAACCCAACGCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: GAACAGGATCAAGGAGATT-GGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|86862869|gb|CI331708.1|CI331708
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|58612576|gb|CK040288.1|CK040288
EST:     AGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: AGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|86840691|gb|CI333939.1|CI333939
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATTCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|88472610|gb|CI409881.1|CI409881
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|29686352|gb|CB682627.1|CB682627
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGTTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|29684749|gb|CB681024.1|CB681024
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|29685611|gb|CB681886.1|CB681886
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|29685612|gb|CB681887.1|CB681887
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|86838940|gb|CI330354.1|CI330354
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATTCCAAGGCAATTTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
EST: gi|88380235|gb|CI516222.1|CI516222
EST:     TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG                         GTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA
genomic: TGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGA

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: 63 (upstream exon), 75 (downstream exon)
Score: 88

CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAGgtgcttcacc ... tttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGAGCCAAGAACGCCGGCCAGGCGCAGGAGTTCGCCGGCGCGCTCGGCTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacagaagtgcagttccactgaaaacagctggtgttttcttttttttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGAGCCAAGAACGCCGGCCAGGCGCAGGAGTTCGCCGGCGCGCTCGGCTGGA
                                 tgttttcttttttttg  CT-rich tract
 ttttcttttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttcacctcatataatgctcagcaaatccatgcaagaaaaggaattaatatctccaagtaggatgagcagcaacttgcaaggaacagaagtgcagttccactgaaaacagctggtgttttcttttttttgtttcagGTTTCACTGAACTGGCTGACATGCCAAGGCAATGTGGTGCCAATCCCCGGAGCCAAGAACGCCGGCCAGGCGCAGGAGTTCGCCGGCGCGCTCGGCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA