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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgaccttgaaactttattatgtctcctcctcccattcctaacaggaaaaacagattaagcaatcacacacaatctcctttttgtag

Basic information

species Zea mays
transcript GRMZM2G129513_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129513_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 5'ss of exon 7
TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgaccttgaaactttattatgtctcctcctcccattcctaacaggaaaaacagattaagcaatcacacacaatctcctttttgtag
|||  ||||||| || || ||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||   |||| || |||   || ||| | |  |      |||  |    |       |  | || |||  | |    |  |  |||||||||
TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacgtt-aaatcgtagtatttgtgatgt----attttt----gtggttttatttcaaacaaata-attggacttgttttttgtag

upper sequence: GRMZM2G129513_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 7
TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgaccttgaaact-ttattatgtctcctcctcc---cattcctaacaggaaaaacag--attaagcaatcac-------acacaatctcctttttgtag
|||  |||| ||| |||||||||| ||||||||||| ||||| ||||||||||| ||||| ||||| ||||| ||||||||||| || ||||| |   | ||||  ||  |||        | |  | |   |||   ||  | ||| || ||  | | |  |||          |  | || |  ||| || ||
TGCATTGATATGTATGAAAAATGCTCCAAACATACCTGCAAAGAACTTTCATGCTTTGACTAGGTTAGATGAGAATAGAGCAAAATGTCAGgttaagtagcttgtgaccattacctcagtccatgatacagtcatgtttattatgaacaaaaggaaatcaataattgttgtatgaattcgatgtgatttgtgcag
















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|211395431|gb|FL283721.1|FL283721
EST:     ANAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGG
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGG
EST: gi|110219294|gb|EC901192.1|EC901192
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|32916975|gb|CF021787.1|CF021787
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|211398041|gb|FL283723.1|FL283723
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|211398042|gb|FL283724.1|FL283724
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|148971653|gb|EE022376.2|EE022376
EST:     AAA-TTTCATGCTTTGACGGGGTGGGATGAAAATAGAGCAAAGTGCCAAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTAT
genomic: AAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCC-AGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTAT
EST: gi|211395432|gb|FL283722.1|FL283722
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|211195516|gb|FL441325.1|FL441325
EST:     AAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|74239371|gb|DT647285.1|DT647285
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|13558383|gb|BG549739.1|BG549739
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
EST: gi|13490961|gb|BG517725.1|BG517725
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAANNNNNNNNACGTGACTAT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAA-GTATCAAACGTGACTAT
EST: gi|30705491|gb|CD058800.1|CD058800
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG                         CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATT

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: 46 (upstream exon), 49 (downstream exon)
Score: 65

TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 906

TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG


Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 8

TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 635

TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgacc ... ctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAGgtgactgaccttgaaactttattatgtctcctcctcccattcctaacaggaaaaacagattaagcaatcacacacaatctcctttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG