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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttcactcggaaccaagtaaatttcctacctccaacataatccactctcgccaccactaacatcagaaactttgcag

Basic information

species Oryza sativa
transcript LOC_Os08g08200.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08200.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G042398_T02 (Zea mays), 5'ss of exon 10
AAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttcactcgg-aaccaagtaaatttcctacctcc-aacataatccactctcgccaccactaacatcagaaactt---tgcag
|| ||||||||||||||||||||||||||||||||||| |||||||| || ||||| |||||||||||||||||||| ||||||||||||||||||||||||||| | | |  |  |||    || ||||  |||| |  ||      |  || |  ||  |   | ||  |     |    |||||
AAGAACTTCCATGAATTTGTACACGAGTACTTGCAAAAACCAGAGTTCGCCGAGCTGATGCGGAGGCTGGGTGCCCTCGGTGATGGAAGGCAGGACCAAAgtaatgtccccctgccaacttcatagattttgtacccctgaatgctgccggcttttccccacctcagcactaatgcgtgaaatgcag

upper sequence: LOC_Os08g08200.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 11
AAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttcactcggaaccaagtaaatttcctacctccaacataatccactctcgccaccac----taacatcagaaactttgcag--------------------------------------------------------------------------------------------------------
|| ||||  |||||||||||  | ||||||||| |||| ||||| |||| |||||| ||||||||||| |||||  | ||||||||||  || ||||| ||||| |   | ||         |   |  | ||  ||     |  ||| |||||  |  | |    || | |     |  |||                                                                                                           
AAGAACTCACATGAATTTGTGGATGAGTACTTGAAAAAACCAGAATTTGTTGAGCTTATGCGGAGGCTAGGTGCTTTGGGTGATGGAAACCAAGACCAGAgtaagtccaattcctgtttgtttccctcccatatatcttttttt-tcccctctcatcttctccccttacccttcttcaacttgtgttctcattctaatgatggaacatttctcatttgccttctgaaattgcatcattttcacatctccaaagagtattgacttttaaaatatcgtctttcaatgtttag
















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|86477891|gb|CI120524.1|CI120524
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCCCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86437177|gb|CI118899.1|CI118899
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88514357|gb|CI441863.1|CI441863
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86413070|gb|CI067475.1|CI067475
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88508690|gb|CI436196.1|CI436196
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTTTCACAGGATGAATGGGAGGTAGCCTATCTTTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|58687919|gb|CK076606.1|CK076606
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86426409|gb|CI071506.1|CI071506
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88542316|gb|CI471638.1|CI471638
EST:     GGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTN
genomic: GGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88834373|gb|CI077656.1|CI077656
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|89175372|gb|CI042393.1|CI042393
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCCAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86428518|gb|CI075199.1|CI075199
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86541036|gb|CI181242.1|CI181242
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88516881|gb|CI444461.1|CI444461
EST:     TCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|87027891|gb|CI276247.1|CI276247
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86433729|gb|CI094072.1|CI094072
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88969123|gb|CI099074.1|CI099074
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88199436|gb|CI199286.1|CI199286
EST:     TGAGCTCATTCGGAGGCTGGGTGCCCTAGGTGGTGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88518293|gb|CI445947.1|CI445947
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTTTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|29689085|gb|CB685360.1|CB685360
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86854764|gb|CI259050.1|CI259050
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88971622|gb|CI388867.1|CI388867
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|25801957|gb|CA757918.1|CA757918
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG

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: 69 (upstream exon), 48 (downstream exon)
Score: 26

AAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTGTTTTGCGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttcactcggaaccaagtaaatttcctacctccaacataatccactctcgccaccactaacatcagaaactttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG