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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgactcttgtttttcatatccgatctgtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA

Basic information

species Oryza sativa
transcript LOC_Os05g49200.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G899123_T01 (Zea mays), 3'ss of exon 2
------------------------gtactgactcttgtttttcatatccgatct-gtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
                        | | ||  | |   ||||  ||||  ||||  | | |||||||||||    || |  | |     | | |     ||||||| ||||||||  |||| ||| |||| || ||||| |||||||| || ||||||||||||||||||
attacaaattgggtattacatactgcaatgtttatatcttttgttatctaatctcatgtcaatgagaaatataactaaatgtgg-----catctatcattatcagGGTTTTGTGCCGGCGGCTGTGCAGCCATGGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G065757_T02 (Zea mays), 3'ss of exon 7
-----gtactgactcttgtttttcatatcc-gatct-gtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
     | | ||  |||   ||||  ||| |  ||||  | | |||||||||||    || |  | |     | | |     ||||||| ||||||||  | || ||| |||| || ||||| |||||||| || ||||||||||||||||||
gtactgcaatgtttctatcttttgttattctaatctcatgttaatgagaaatataactaaatgtgg-----catctatcattatcagGGTTTTGTGCCGGTGGCTGTGCAGCCATCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G370357_T01 (Zea mays), 3'ss of exon 5
-----gtactgactcttgtttttcatatccgatct-gtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
     | | ||  | |   ||||  ||||  ||||  | | |||||||||||    || |  | |     | | |     ||||||| ||||||||  |||| ||| ||||||| ||||| |||||||| || ||||||||||||||||||
gtactgcaatgtttatatcttttgttatctaatctcatgtcaatgagaaatataactaaatgtgg-----catctatcattatcagGGTTTTGTGCCGGCGGCTGTGCAGCTATGGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G153977_T01 (Zea mays), 3'ss of exon 1
------------gtactgactcttgtttttc-atatccgatct-gtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
               ||     ||||| ||| ||||    |||  | | |||||||||||    || |   ||| |    | | | | | ||||| ||||||||| | |||||| |||| |||||||| |||||||| || ||||||||||||||||||
gcaggccaggttcctctcttctttgttattctatataatgtctcatgttaatgagaaatataactaaatg-cgtca----tctaccgttgtcagGGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G001713_T01 (Zea mays), 3'ss of exon 3
-----gtactgactcttgtttttcatatccgatct-gtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
     ||| ||  | |   ||||  ||||  ||||  | | |||||||||||    || |  | |     | | |     ||||||| ||||||||  |||| ||| |||| || ||||| |||||||| || |||||||||||||||| |
gtactgtaatgtttatatcttttgttatctaatctcatgtcaatgagaaatataactaaatgtgg-----catctatcattatcagGGTTTTGTGCCGGCGGCTGTGCAGCCATCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCATA

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G057724_T01 (Zea mays), 3'ss of exon 10
-----gtactgactcttgtttttcatatccgatct-gtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
     | | ||  | |   ||||  ||||  ||||  | | |||||||||||    || |  | |     | | |     ||||||| ||||||||  |||| ||| ||||| | ||||| |||||||| || ||||||||||||||||||
gtactgcaatgtttatatcttttgttatctaatctcatgtcaatgagaaatataactaaatgtgg-----catctatcattatcagGGTTTTGTGCCGGCGGCTGTGCAGCTGTCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G035636_T01 (Zea mays), 3'ss of exon 7
-----gtactgactcttgtttttcatatccgatct-gtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
     | | ||  | |   ||||  ||||  ||||  | | |||||||||||    || |  | |     | | |     ||||||| ||||||||  |||| ||| |||| || ||||| |||||||| || ||||||||||||||||||
gtactgcaatgtttatatcttttgttatctaatctcatgtcaatgagaaatataactaaatgtgg-----catctatcattatcagGGTTTTGTGCCGGCGGCTGTGCAGCCATCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA

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|33795396|gb|CF323568.1|CF323568
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|29687282|gb|CB683557.1|CB683557
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|58668482|gb|CK057168.1|CK057168
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|33683538|gb|CF311777.1|CF311777
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|58596651|gb|CK007179.1|CK007179
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|125863426|gb|EL586708.1|EL586708
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|29675128|gb|CB671403.1|CB671403
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|58658759|gb|CK047439.1|CK047439
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAACGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|86908029|gb|CI298797.1|CI298797
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|29637768|gb|CB642777.1|CB642777
EST:     GCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: GCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|58668099|gb|CK056785.1|CK056785
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|29657722|gb|CB653997.1|CB653997
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTAT
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTAT
EST: gi|29660989|gb|CB657264.1|CB657264
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|29627821|gb|CB632832.1|CB632832
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|55827430|gb|AU030192.2|AU030192
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|218478948|gb|FG952780.1|FG952780
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|218480608|gb|FG959514.1|FG959514
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|58681561|gb|CK070248.1|CK070248
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|29644200|gb|CB649207.1|CB649207
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|218495569|gb|FG950148.1|FG950148
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|88396547|gb|CI601030.1|CI601030
EST:     TTTGAGATGGGCGATGTCCTGATTGGGGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|86847366|gb|CI286963.1|CI286963
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|33381232|gb|CF196575.1|CF196575
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|58599924|gb|CK010452.1|CK010452
EST:     GGCAGTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATNAGCAGACTCTGGAACATCATTG
genomic: GGCAGTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTAT-AGCAGACTCTGGAACATCATTG
EST: gi|218481767|gb|FG945139.1|FG945139
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|218486960|gb|FG945468.1|FG945468
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|218484121|gb|FG947440.1|FG947440
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|29639939|gb|CB644948.1|CB644948
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
EST: gi|428757|gb|D24912.1|D24912
EST:     TTTGAGATGGGCGATGTCCTNATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCT
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCT
EST: gi|66924030|gb|CX110878.1|CX110878
EST:     TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG                         GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC
genomic: TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGC

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: 60 (upstream exon), 65 (downstream exon)
Score: 271

TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAGgtactgactc ... ctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA
                     atcttac  putative branch site (score: 271)
                                       cctttgct  putative PPT
        taaatgagaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgactcttgtttttcatatccgatctgtctaaatgagaaataatcttacacatcgttacacctttgctgctatcagGATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT