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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcaaattttacatgccatttacctttctttcttaattgctgaacttattggaatatcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAAGGTCTCTTAACTACACGATG

Basic information

species Oryza sativa
transcript LOC_Os05g38150.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G375504_T02 (Zea mays), 3'ss of exon 17
-----------------------------------------------------gtacttcaaattttacatgccatttacctttctt-tcttaattgctgaacttattggaatatcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAAGGTCTCTTAACTACACGATG
                                                      |  |     || |      |||||||  ||||| |||| ||   |  || |    ||||||||||| |||||||||||||||||||||||||| ||||| || || || ||||||||||||||||||||||| ||||| ||
gtacgccctatctttggagtaaatgggattatttgattacatcggcatgcattatgttatcttttctggtgatcatttactgttcttatcttcatatttctacctt---gaatatcttgagtagGTTGGCATAAGCACAGGGCGTATACATGCTCGCGGGCCTGTGGGTGTTGAAGGTCTCTTAACAACACGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G061777_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------gtacttcaaatttta-catg-ccatttacctttctttcttaattgctgaacttattggaatatcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAAGGTCTCTTAACTACACGATG
                                                                      |  || |  ||||  ||||    |||||| || | |    ||| ||  || | ||| |||||||| |||||||||||||||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| || || ||
gtaggtcctatctttttatatggcatttgagtgaactctttggaaaagaatgtcttggcataagttacttttttttatcttttctcatgattgtttaccgttatcttcatatttct--acct-ttgaaatatcttaaatagGTTGGCATAAGCACAGGGCGTATACATGCTCGTGGGCCCGTGGGTGTTGAAGGTCTCTTAACAACGCGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G061777_T02 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------gtacttcaaatttta-catg-ccatttacctttctttcttaattgctgaacttattggaatatcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAAGGTCTCTTAACTACACGATG
                                                                      |  || |  ||||  ||||    |||||| || | |    ||| ||  || | ||| |||||||| |||||||||||||||||||||||||||| ||||| ||||| || |||||||||||||||||||||           
gtaggtcctatctttttatatggcatttgagtgaactctttggaaaagaatgtcttggcataagttacttttttttatcttttctcatgattgtttaccgttatcttcatatttct--acct-ttgaaatatcttaaatagGTTGGCATAAGCACAGGGCGTATACATGCTCGTGGGCCCGTGGGTGTTGAAGGTCTCTTA-----------

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|86851167|gb|CI312568.1|CI312568
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|88261913|gb|CI365489.1|CI365489
EST:     ATGCAAGTACGAAATTCTCTGAT-GGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGGCCCGT-GACCAGTGGGTGTTGA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCAT-GCCCGTGGACCAGTGGGTGTTGA
EST: gi|89187311|gb|CI047378.1|CI047378
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|86431434|gb|CI085045.1|CI085045
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGTACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|66915778|gb|CX102626.1|CX102626
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|88253863|gb|CI352489.1|CI352489
EST:     TGCAAGTACGAGATTCTCTGATGGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: TGCAAGTACGAGATTCTCTGAT-GGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|88485232|gb|CI422503.1|CI422503
EST:     TTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: TTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|25798187|gb|CA754084.1|CA754084
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|88262625|gb|CI366399.1|CI366399
EST:     ATGCAACTACGAGATTCTCTTATGGGGCTCCTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|88274920|gb|CI388378.1|CI388378
EST:     TTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: TTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|163917821|gb|EG712147.1|EG712147
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|86887353|gb|CI313256.1|CI313256
EST:     ATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|89178281|gb|CI391460.1|CI391460
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCCTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|87029670|gb|CI257465.1|CI257465
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|88272298|gb|CI386752.1|CI386752
EST:     TGGGTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: TGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|89193653|gb|CI116286.1|CI116286
EST:     ATGCAAGTACGAGATTCTCTGATGGGGCTCTTTTTGGATTGGTTGCTGAG                         GTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: ATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA
EST: gi|88262529|gb|CI366303.1|CI366303
EST:     TCTGATGGGGCTCGTTTTGGATTTGGTGCTGAG                         G-TGGCATAAGCACA-GGC-TAGCCATGCCCGTGGACCAGTGGGTGTTGAA
genomic: TCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAA

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: 66 (upstream exon), 63 (downstream exon)
Score: 14

TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAGgtacttcaaa ... tcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAAGGTCTCTTAACTACACGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgccatttacctttctttcttaattgctgaacttattggaatatcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAAGGTCTCTTAACTACACGATG
                   tcttaat  putative branch site (score: 14)
             tttctttcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttcaaattttacatgccatttacctttctttcttaattgctgaacttattggaatatcttgaatagGTTGGCATAAGCACAGGGCGTATCCATGCCCGTGGACCAGTGGGTGTTGAAGGTCTCTTAACTACACGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG