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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggccccaagattattcaaatcaaggcatttcagactatcagcatttttctttctgagaaattcatattatcatggattcatctcttgaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG

Basic information

species Oryza sativa
transcript LOC_Os07g39630.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 8
taatggccccaagattattcaaa-tcaaggcatttcagactatcagcatttttctttctgagaaattcatattatcatggattcatctcttgaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
  | |      |  | || ||   |  | || ||  |  ||   || |  |   | |   |           | |||    || |    ||   ||  |||||||| || |||||||||||||||||||||||||| |||||||||
-gaggtagtacatgtcatccacgcttgaagcgttctacccttcaagtaagtccttgtactatttgccgcccctctcaactttttagtgtttattttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
















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|38473913|gb|CF958045.1|CF958045
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCGGATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|29675062|gb|CB671337.1|CB671337
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|218481593|gb|FG960934.1|FG960934
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|29673566|gb|CB669841.1|CB669841
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|86500993|gb|CI143626.1|CI143626
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|88226063|gb|CI225979.1|CI225979
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCCAAAATATTCAAATGTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAAT-TGAAGCATTTCATGTGTTCAAG
EST: gi|38481075|gb|CF965164.1|CF965164
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|29673647|gb|CB669922.1|CB669922
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|89170800|gb|CI040077.1|CI040077
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGT-GTTCAAG
EST: gi|29679531|gb|CB675806.1|CB675806
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|87008328|gb|CI301086.1|CI301086
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|29664684|gb|CB660959.1|CB660959
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGC-AAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|58663168|gb|CK051854.1|CK051854
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|25799534|gb|CA755495.1|CA755495
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|29656023|gb|CB652298.1|CB652298
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|66915714|gb|CX102562.1|CX102562
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|58688748|gb|CK077435.1|CK077435
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|29660229|gb|CB656504.1|CB656504
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
EST: gi|86426306|gb|CI071403.1|CI071403
EST:     GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA                         GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
genomic: GTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG

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: 51 (upstream exon), 45 (downstream exon)
Score: 42

TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGAgtaagttcac ... gaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttctttctgagaaattcatattatcatggattcatctcttgaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
                                       tctcttg  CT-rich tract
                aaattcatattatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatggccccaagattattcaaatcaaggcatttcagactatcagcatttttctttctgagaaattcatattatcatggattcatctcttgaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggat