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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggattccgccttatgcctttctttatgaagtttgctacccttttttttttacataaattggaaaaatgtatgtgctattcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g59930.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 2
gtttggattccgccttatgcctttctttatgaagtttgctacccttttttttttacataaattggaaaaatgtatgtgctattcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG
|||| ||||| ||||| | ||||  |||     | ||  |||    ||| ||| || || ||  |       | | |  | ||  |  ||||||||||| |||||||| |||||||||||||| |||||||||||||||||||||||||||||||| ||  ||||||||||||| || |||
gttttgattctgccttttcccttaatttt----gctt-ttacatcatttctttaac-tatatctgtgt----tctcttgtttttatgcagAGGACAAGACGCTACAGGTGAAGAAGTAATCAAGCCTTATACCCCTACTACATTGGATTCTGATCTTGGATATTTTGAGCTTGTCATAAAG

upper sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 2
--------------gtttggattccgccttatgcctttctttatgaagtttgctacccttttttttttacataaattggaaaaatgtatgtgctattcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG
               |  | ||  |      ||  |   ||| | |  ||   || |  | |||||||    |  |||  || |   |    ||  ||    || ||  ||||||||  ||| ||||| || |||||||| ||||||||||||||||||||||| ||| | || |||||||| || |||||||||
tataatgataactaatgagtataacaggaattgtttccattttttagtttctttatcaatgtttttttgt-catcttgtgaataaaca---acttctcaaacagGGGTAAAGATGCTCAAGGTGAAGACGTTATCAAACCATATACCCCTACTACATTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG

upper sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 2
--------gtttggattccgccttatgcctttctttatgaagtttgctacccttttttttttacataaattggaaaaatgtatgtgctattcttt--tagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG
         | |  || |      |||    | |||      |    |   ||  | |   | | | |        ||| |  |   | ||||     || ||  | |||| |   ||  ||||| | |||||||| |||||||| |||||||||||||||||| | ||  ||||||| |||||||| |||
ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatcctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG

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|88362855|gb|CI614211.1|CI614211
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
EST: gi|88763102|gb|CI772658.1|CI772658
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCG
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCG
EST: gi|117244284|gb|CT843075.1|CT843075
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
EST: gi|58685456|gb|CK074143.1|CK074143
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
EST: gi|58684839|gb|CK073526.1|CK073526
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
EST: gi|88736272|gb|CI759780.1|CI759780
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCA
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCA
EST: gi|58595179|gb|CF993487.1|CF993487
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
EST: gi|88388215|gb|CI627754.1|CI627754
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATAC
EST: gi|2309816|gb|C25971.1|C25971
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTTCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATA
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATA
EST: gi|58603188|gb|CK013716.1|CK013716
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
EST: gi|427743|gb|D23879.1|D23879
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTAC
EST: gi|88391603|gb|CI600792.1|CI600792
EST:     ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAG                         AGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTA
genomic: ACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTA

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: 75 (upstream exon), 66 (downstream exon)
Score: 69

AAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAACCTCTGTATTGGGCCTTCCAATTGGTCAGCATATCAGTTGCAGgtttggattc ... attcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctacccttttttttttacataaattggaaaaatgtatgtgctattcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG
                                           ctattctttt  CT-rich tract
         ttttttttttacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggattccgccttatgcctttctttatgaagtttgctacccttttttttttacataaattggaaaaatgtatgtgctattcttttagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT