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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgcaacttttcaattttattctgctgaagtacgtatgttaacatctctgttctgctttctgctgtgtag

Basic information

species Zea mays
transcript GRMZM2G088140_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088140_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 12
TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgtt-agtctgcaacttttcaattt--tattctgctgaagtacgtatgttaacatctctgttctgctttctgctgtgtag
|||||| ||||||||||| |||||| ||||||||||||||||||| ||||| |||||||| ||||| || || |||||||||| ||||| |||| ||||||||  || |   | | |||  | |  |  | | ||||| ||  ||  ||||||    |  | || ||| || | |||||
TGCTGAAGTTTTAAAGCAAGAAAATACTTCACTTAGAGATGAAGTGAACCGGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttctcattcttcgctctcttgctattctgaaatatatactttaacactgtt--tttgttttttgttctgtag
















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|60358086|gb|DN225059.1|DN225059
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|60345747|gb|DN212720.1|DN212720
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|60350100|gb|DN217073.1|DN217073
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|32867163|gb|CF006845.1|CF006845
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211353575|gb|FL066643.1|FL066643
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|60337844|gb|DN204817.1|DN204817
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|32834586|gb|CD974264.1|CD974264
EST:     ACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: ACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|60353486|gb|DN220459.1|DN220459
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|32832648|gb|CD972326.1|CD972326
EST:     TACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: TACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211496290|gb|FL041702.1|FL041702
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|71772544|gb|DR970475.1|DR970475
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211091177|gb|FL442412.1|FL442412
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCTGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|32834651|gb|CD974329.1|CD974329
EST:     ACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: ACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211088628|gb|FL437494.1|FL437494
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCTGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|32931454|gb|CF036266.1|CF036266
EST:     GTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211467879|gb|FL454207.1|FL454207
EST:     GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCTGGACTTAACAAC
genomic: GTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC

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), 48 (downstream exon)
Score: 362

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGTGATGACAGCCAGAAAAAAGGAAACTAATGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGTGATGACAGCCAGAAAAAAGGAAACTAATGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 161

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGTGATGACAGCCAGAAAAAAGGAAACTAATGCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 197

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgc ... tgctgtgtagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGTGATGACAGCCAGAAAAAAGGAAACTAATGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgttagtctgcaacttttcaattttattctgctgaagtacgtatgttaacatctctgttctgctttctgctgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA