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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatatttttgtatacatgattacaatggttttctcttgttgctattcaaacccttgagaagtaataaatcctcaatttatcatgtattgcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG

Basic information

species Zea mays
transcript GRMZM5G883741_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G883741_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g44520.1 (Oryza sativa), 3'ss of exon 28
--------caaatatttttgtatacatgattacaatggttttctcttgttgctattcaaacccttgagaagtaataaatcctcaatttatcatgtattgcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG
         || |   ||| | |   |   || |||||| || |||  |||| ||  |||  | |  | | |||||    ||  |  |    |  ||||  |||  ||||||||||||||||||||||||| |||||  || |||| |||  ||||||||| ||||||||| | ||| | | |||||| | |||||| |||
acctgttttaagttaatttattt---taggtaaaatggtatt-tctgattgcaatataaaatcgtagggaataatactgtcttgacat----taaattgattgatcagGTTCGAGACACCAAGATAAAGTTCCTTTCTGGCTTTAATCAAGAAACTGAGGATGACAAGTCTTCTTGGACGGCACTTGTTGCTTCTCTTAAG
















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|32847415|gb|CD987096.1|CD987096
EST:     TACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: TACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|60346566|gb|DN213539.1|DN213539
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|67023455|gb|CO452204.1|CO452204
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|60344958|gb|DN211931.1|DN211931
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|33097382|gb|CF057342.1|CF057342
EST:     ACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCCTTCCAGCGTTAAGCAACTAACTGAG
genomic: ACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|166433010|gb|EG122598.1|EG122598
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAAC
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAAC
EST: gi|14245659|gb|BG874241.1|BG874241
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|5686780|gb|AI939873.1|AI939873
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|60355778|gb|DN222751.1|DN222751
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|211490738|gb|FL282854.1|FL282854
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
EST: gi|16379794|gb|BI993153.1|BI993153
EST:     AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAG                         GTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG
genomic: AGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAG

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: 294

GTTGATGATAAAGAAAAGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

GTTGATGATAAAGAAAAGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 569

GTTGATGATAAAGAAAAGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GTTGATGATAAAGAAAAGGGGGTTTTAGTTGGTACAAAGAGCATACCTGAACAGTTAGATGAGGAGgttggtgcac ... gcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaaacccttgagaagtaataaatcctcaatttatcatgtattgcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG
                              aatttatcatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatatttttgtatacatgattacaatggttttctcttgttgctattcaaacccttgagaagtaataaatcctcaatttatcatgtattgcatgactagGTTCGAGACACCAAGATAAAGTTTCTTTCCAGCGTTAAGCAACTAACTGAGGAGGACAAGTCTGCCTGGTCAGAACTTGTGGTTTCTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG