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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtagaagccgaccatctgttaatcctgagttttcactttcctgtcccaagaaataaggcgtcagatccactcaaatatgtagagtaaacttcacagcagattttctaaatcattggtatcatatgaacttcttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTACTGCTGGATGAGGCCAGAGGATATCGATTACCCCAGACCTGTCACTGAGT

Basic information

species Oryza sativa
transcript LOC_Os03g52630.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 2
gttggtagaagccgaccatctgttaatcctga--gtt--ttcactttcctgtcccaagaaataaggcgtcagatcca---ctcaaatatgtagagtaaacttcacagcag-attttctaaatcattgg-tatcatatgaac--ttcttattgc----agGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTACTGCTGGATGAGGCCAGAGGATATCGATTACCCCAGACCTGTCACTGAGT
|||||||| | |  | ||   | | ||| ||   | |  ||  || |   || | ||| ||   | | |||||||||   |      ||      || |   |||| | |        | | |  ||  |  | ||| |||  |||| | |||    |||||||||||||||||||||| |||||  |    || ||||| ||||| ||||||||||||||||||||||| ||||| |||   || || ||||| ||||
gttggtagcaac--aacaatagatcatcttggcggctgatttgctctgtcgtgcaaagcaactggtcatcagatccagtaccttggcatcctttctacagcacacatctgcggacagcagaccgctgactcccgtatcaacacttctcaatgcgtgcagGTGGGTGTAGGTGACACCTCTAAAGGCAGCAGTCAGCCTAACGACCATTACTGCTGGATGAGGCCAGAGGACATCGACTACAAGAGGCCGGTCACCGAGT

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 2
gttggtagaagccgaccatctgttaatcctgagttttcactttc-ctgtcccaagaaataaggcgtcagatccactcaaatatgtagagtaaacttcacagcagattttctaaatcattggtatcatatgaacttcttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTACTGCTGGATGAGGCCAGAGGATATCGATTACCCCAGACCTGTCACTGAGT
||||||||     || |||||      | |||    | | || | ||||||||||||||  | | ||||||||||  ||  |          ||| ||      | ||                        ||  ||||||||||||||||||||||||||||| |||||  |    || ||||||||||| |||||||||||||| |||||||| ||||| |||   || || ||||| ||||
gttggtagccatagatcatctt----gcttgatggctgatttgctctgtcccaagaaattggtcatcagatccaccaaaccact-------gactacaacatgaactt------------------------ctcgttattgcagGTGGGTGTAGGTGACACCTCTAAAGGCAGCAGTCAGCCTAATGACCATTACTGCTGGATGAGACCAGAGGACATCGACTACAAAAGGCCAGTCACCGAGT
















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|58674076|gb|CK062762.1|CK062762
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|88361349|gb|CI626453.1|CI626453
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|33676216|gb|CF304455.1|CF304455
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|27553984|gb|CA997884.1|CA997884
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|58664223|gb|CK052909.1|CK052909
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|58690204|gb|CK078891.1|CK078891
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|58669612|gb|CK058298.1|CK058298
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|58609592|gb|CK037625.1|CK037625
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|29634446|gb|CB639455.1|CB639455
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|13447512|gb|AU181006.1|AU181006
EST:     TATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|58665452|gb|CK054138.1|CK054138
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|29674435|gb|CB670710.1|CB670710
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|58662741|gb|CK051427.1|CK051427
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
EST: gi|58669114|gb|CK057800.1|CK057800
EST:     TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAG                         GTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC
genomic: TCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTAC

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), 75 (downstream exon)
Score: 122

TGAGCTCGACCATGTCAAGGAGCTGATCAAGTGGGGCACAGATTACCTCCTCAAGACCTTCAATTCATCAGCCGATACTATCGATCGGATCGTCGCACAGgttggtagaa ... cttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTACTGCTGGATGAGGCCAGAGGATATCGATTACCCCAGACCTGTCACTGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttcacagcagattttctaaatcattggtatcatatgaacttcttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTACTGCTGGATGAGGCCAGAGGATATCGATTACCCCAGACCTGTCACTGAGT
                 ttctaaa  putative branch site (score: 122)
                                          cttcttatt  putative PPT
              attttctaaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtagaagccgaccatctgttaatcctgagttttcactttcctgtcccaagaaataaggcgtcagatccactcaaatatgtagagtaaacttcacagcagattttctaaatcattggtatcatatgaacttcttattgcagGTGGGTGTAGGTGACACCTCAAAAGGTGGTGCCCAACCTAATGACCACTACTGCTGGATGAGGCCAGAGGATATCGATTACCCCAGACCTGTCACTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT