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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAAGAGTAAAGGCAGCATCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatccttttattgtgctatgccctctgaatcactaattagtgtttcaatactagcatactattgtcagagacacgtaggcccatttctgtgcattttgtaaaggttctttcaatggtagtgtagagtaacatccccattttgtag

Basic information

species Oryza sativa
transcript LOC_Os11g03470.4
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 10
GTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAAGAGTAAAGGCAGCATCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatccttttattgtgctatgccctctgaatcactaattagtgtttcaatactagcatactattgtcagagacacgtaggcccatttctgtgcattttgtaaaggttctttcaatggtagtgtagagtaacatccccattttgtag
|||||||||| || ||||| || ||||| ||||||||| | |  |||||||||| || |||||| ||||||||||| |||||| ||||||||||| ||||||| | ||||      |  ||  ||   |   | | |||     || |      | ||||||          || | |  |    | ||||    |  ||     | ||||  || |                                 
GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatccagc--ctaggccctggtgtgatagt-actgtgcggtatcc----attagcat----------gaaaaaaatcaatctattttctggagttacagcatggtttattga---------------------------------
















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|88257730|gb|CI360316.1|CI360316
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|29685332|gb|CB681607.1|CB681607
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|89163490|gb|CI100380.1|CI100380
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|88291219|gb|CI527609.1|CI527609
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|86879665|gb|CI327232.1|CI327232
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCT-TAAGATTGAAAGCACA-G                         GTGGCCAAGTGGGCCTTGAAGAACTCCCG-AAAACTCTGCACTGGGAAGGT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGT-GCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGT
EST: gi|88460564|gb|CI532037.1|CI532037
EST:     CGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: CGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|86535227|gb|CI175433.1|CI175433
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|88964320|gb|CI045513.1|CI045513
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|86601034|gb|CI356791.1|CI356791
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|88966008|gb|CI006763.1|CI006763
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|89163605|gb|CI100495.1|CI100495
EST:     TCTTTGAAAGGAAATGTTCTTCGCTAGGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|86491794|gb|CI134427.1|CI134427
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|86604043|gb|CI114817.1|CI114817
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|86491655|gb|CI134288.1|CI134288
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|88463800|gb|CI527127.1|CI527127
EST:     CTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: CTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|86480044|gb|CI122677.1|CI122677
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
EST: gi|89195888|gb|CI007307.1|CI007307
EST:     TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGG                         GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT
genomic: TCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTT

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: 59 (upstream exon), 64 (downstream exon)
Score: 14

GTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAAGAGTAAAGGCAGCATCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatcc ... cattttgtagGTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAAGAGTAAAGGCAGCATCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatccttttattgtgctatgccctctgaatcactaattagtgtttcaatactagcatactattgtcagagacacgtaggcccatttctgtgcattttgtaaaggttctttcaatggtagtgtagagtaacatccccattttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA