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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgacattcagataaagtaggggattacctatctttaatattttctagttgctcccatctttctttgatttcagcttattttgctattgttctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG

Basic information

species Zea mays
transcript GRMZM5G825854_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825854_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os08g34970.1 (Oryza sativa), 3'ss of exon 21
gcgacattcagataaagtaggggatta-cctatctttaatattttctagttgctcccatct----ttctttgat-----ttcagcttattttgctattgtt-ctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG
           ||||| || || |  |  |||   | | |  ||| ||| ||| |  |||     || ||| ||     ||||||| |||||| || |  |  | |||||||| ||||| |||||||| ||| |||||||||||||||||||||||||||| || ||||||||||| || ||||||||||||||||||||||||
-----------ataaaataaggcagcagtctaatgtgattgctttgtagatgcccatatcctcgattttttaatattttttcagctaattttgttactactattttttcagGAATTGGAAAAAAGCCTCAAATCTACCTGTGAAGAGTTTATAATGTCCATTACAAAATTAGTAGTGGATCCAATGCTTTCTTTTGTTACTAAG

upper sequence: GRMZM5G825854_T01 (Zea mays), 3'ss of exon 21
lower sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 22
----gcgacattcagataaagtaggggattacctatctttaatattttctagttgctcccatctttctttgatttcagcttattttgctattgttctattt-cagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG
      || |||  |   | ||| |   |   | || | |   |     | | ||        |  | |  | |  | | |   |    |||| | ||||| |||||  ||||||||||||| ||||| || ||||| |||||||| |||||  | |||||  |||| || || || |||||||| ||||||||||||
atattagaaatttggtgtacgtatgaagtgcacaatttgttggaccaatttgatgtgt-----tgccatgcaatgtaacatgggtgatcattggtttatttgcagGAACTGGAGAAAAGCCTCAAAGCCACTTGTGAGGAGTTTATTATGTCGGTCACTAAGCTAGTTGTGGATCCCATGCTTTCATTTGTTACTAAG
















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|32832225|gb|CD971903.1|CD971903
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|32929996|gb|CF034808.1|CF034808
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|6102001|gb|AW126471.1|AW126471
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|37386459|gb|CF630415.1|CF630415
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|32931787|gb|CF036599.1|CF036599
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCTATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA

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: 45 (upstream exon), 49 (downstream exon)
Score: 239

TCTCAGGGGTCAGGTCTCATTATTTGATTGGTCCAGGTCAACATCACTAGCTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 229

TCTCAGGGGTCAGGTCTCATTATTTGATTGGTCCAGGTCAACATCACTAGCTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 145

TCTCAGGGGTCAGGTCTCATTATTTGATTGGTCCAGGTCAACATCACTAGCTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 324

TCTCAGGGGTCAGGTCTCATTATTTGATTGGTCCAGGTCAACATCACTAGCTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgctcccatctttctttgatttcagcttattttgctattgttctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG
                 ctttgat  putative branch site (score: 324)
                                            ttctatttc  putative PPT
                              ttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgacattcagataaagtaggggattacctatctttaatattttctagttgctcccatctttctttgatttcagcttattttgctattgttctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATAACTAAATTAGTAGTTGACCCAATGCTTTCTTTTGTTACTAAG

- -acattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgct