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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatacactgctattgaagaacttggattgactattatttctggtttataatcattaaacgatggtcttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG

Basic information

species Zea mays
transcript GRMZM2G136769_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136769_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g39620.1 (Oryza sativa), 3'ss of exon 7
gtgagtatacactgctattgaagaacttggattgactattatttctggtttataatcattaaacgatggtcttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG
  |  | || | |     | |  | |||  ||    | || | ||   |   |||| ||      |   |  |  |||||| |||||||| || || ||||| |||||||| |||||||||| ||| ||||||||||| |||||||| |||||||| ||                     
--gtttgtatagtaactcttatcatcttccat--gtttttgtatc--atcactaattatggttttacacttgtgattcagTTCCACCGGAAGAACTGTATGCAACACAGCTCACTCAGCTCCGAGAGATGGGTTTCATCGACACTGCAGAGAACATCCAG--------------------

upper sequence: GRMZM2G136769_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g39620.6 (Oryza sativa), 3'ss of exon 5
gtgagtatacactgctattgaagaacttggattgactattatttctggtttataatcattaaacgatggtcttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG
  |  | || | |     | |  | |||  ||    | || | ||   |   |||| ||      |   |  |  |||||| |||||||| || || ||||| |||||||| |||||||||| ||| ||||||||||| |||||||| |||||||| || || ||  |||| || |||||
--gtttgtatagtaactcttatcatcttccat--gtttttgtatc--atcactaattatggttttacacttgtgattcagTTCCACCGGAAGAACTGTATGCAACACAGCTCACTCAGCTCCGAGAGATGGGTTTCATCGACACTGCAGAGAACATCCAGGCGCTAGTCGCAACTGCTGG
















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|31356688|gb|CD441045.1|CD441045
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|211474441|gb|FL187197.1|FL187197
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|5777313|gb|AI974932.1|AI974932
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|24764824|gb|CA399986.1|CA399986
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|5791100|gb|AI977892.1|AI977892
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|60343852|gb|DN210825.1|DN210825
EST:     AAATACTTCCAATG                         TGCCACCGGGGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: AAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|31350418|gb|CD434775.1|CD434775
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|5922365|gb|AW055654.1|AW055654
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTATTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|71299524|gb|DR785772.1|DR785772
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTTTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|111990499|gb|EE331933.1|EE331933
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|24765744|gb|CA400903.1|CA400903
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|24769335|gb|CA404464.1|CA404464
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|67040170|gb|CO466425.1|CO466425
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|67035271|gb|CO463804.1|CO463804
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTC-AAATACTTCCA-TG                         TGCCACCGGAG-AGCTCTATGC-ACACAGCTTA-TCAGCTC-AAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|18173213|gb|BM348601.1|BM348601
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
EST: gi|24768442|gb|CA403571.1|CA403571
EST:     CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATG                         TGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG
genomic: CAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

GTACGCCTGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 112

GTACGCCTGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 104

GTACGCCTGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 61

GTACGCCTGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGTGGGCTTGGTTCGGGAGGTGGCATAGGTGTTCCAAATACTTCCAATGgtgagtatac ... cttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggattgactattatttctggtttataatcattaaacgatggtcttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG
    gattgac  putative branch site (score: 61)
                                            tcttatttc  putative PPT
           tattatttctggttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatacactgctattgaagaacttggattgactattatttctggtttataatcattaaacgatggtcttatttcagTGCCACCGGAGGAGCTCTATGCCACACAGCTTACTCAGCTCCAAGAAATGGGTTTCATTGACACTGCGGAGAACATTCAAGCACTGCTCGCTACCGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA