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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacttattctaccaatttcttgatcttgaccctgtagggatttcaaattgacgtgttaaataattttatgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA

Basic information

species Zea mays
transcript GRMZM2G163193_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163193_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 8
gtaaaacttattctaccaatttcttgatcttgaccctgtagggatttcaaattgacgtgttaaataattttatgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA
|| | | || |||| |   ||| |      | | | || ||   |||||  ||||  ||  |  |  |||||  |||||||| |||||||||||||| || ||||||||||||||||||||||||||| ||| |||||||||||| |||||||| ||||||||||||  ||| || ||||| 
gtgagaattcttctgctcctttttaa----taagcatgcagcattttcag-ttgatttgacat-tctttttacactatacagGGCAGACCTTGCAAATTTAGTAAATGAAGCTGCTTTGTTGGCTGGGAGATCAAATAAAGAAATAGTGGAAAAAATTGACTTCATCTGTGCAGTGGAGCGC

upper sequence: GRMZM2G163193_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 8
-------gtaaaactt----attctaccaatttcttgatcttgaccctgtagggatttcaaattgacgtgttaaataattt------tatgctat-acagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA
       ||||||  |    ||||||   || | ||   |       |  |  ||    ||||  |  | || | ||  ||      ||    || |||||||||| ||||||||| | |||||||| ||||||||  |||||||  ||  ||||||||   | ||||| ||  |||| |||||||| || || ||| ||
gacttttgtaaaatcttacgattctatttatgttttttaccccctttttgatcgaaggtaaatccatattttgactaccttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA

upper sequence: GRMZM2G163193_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 8
-------gtaaaactt----attctaccaatttcttga-------tcttgaccctgtagggatttcaaattgacgtgttaaataattttatgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA
       ||||||  |    ||||||   ||   |||        | |||| |        || |  | ||    |        ||||    |  ||||||||||| ||||||||| | |||||||| ||||||||  |||||||| ||  ||||||||   | ||||| ||  |||| |||||||| || || ||  ||
gaattttgtaaaatcttgcaattctatttatgatttgtaccccctttttgatcggaggtaaatattgattttgactaccctgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGGAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAAAGA

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|32825031|gb|CD964753.1|CD964753
EST:     GATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGG                         AGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT
genomic: GATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT
EST: gi|211271702|gb|FL183888.1|FL183888
EST:     AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGG                         AGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTTGTTGGCTGGGCGAT
genomic: AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGC-TTTGTTGGCTGGGCGAT
EST: gi|211378707|gb|FL467950.1|FL467950
EST:     AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGG                         AGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT
genomic: AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT
EST: gi|211271700|gb|FL183886.1|FL183886
EST:     AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGG                         AGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT
genomic: AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT
EST: gi|32807497|gb|CD959731.1|CD959731
EST:     GATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGG                         AGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCG
genomic: GATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCG
EST: gi|211271701|gb|FL183887.1|FL183887
EST:     AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGG                         AGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT
genomic: AAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATT

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: 48 (upstream exon), 49 (downstream exon)
Score: 69

GAGAATCAATTCTAAAAGTTCATGTGAGCAGAAGAGAGCTTCCACTGAGTAAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 95

GAGAATCAATTCTAAAAGTTCATGTGAGCAGAAGAGAGCTTCCACTGAGTAAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

GAGAATCAATTCTAAAAGTTCATGTGAGCAGAAGAGAGCTTCCACTGAGTAAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

GAGAATCAATTCTAAAAGTTCATGTGAGCAGAAGAGAGCTTCCACTGAGTAAAGATGTAGATCTAGCCGATATTGCTGCAATGACAACTGGTTTTACTGGgtaaaactta ... tgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgaccctgtagggatttcaaattgacgtgttaaataattttatgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA
                      aattgac  putative branch site (score: 110)
                              tgttaaataattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacttattctaccaatttcttgatcttgaccctgtagggatttcaaattgacgtgttaaataattttatgctatacagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA