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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctacaattctaccataaaccagccttcctatgtgtagaacaatctctattttcaatggttttgagtcatttatgggttcctttgttcataatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os06g30460.4 (Oryza sativa), 3'ss of exon 13
-tcta-caattctaccataaaccagccttcctatgtgtagaacaatctctattttcaatggttttgagtcatttatgggttcctttgttcataatcact-cagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG
  ||| || || |   |||  || |  || | |  | || |  | |||  || || | ||||| ||||  ||     | || | ||  ||   ||||||  ||||||||||| |||||||||||||| | |||||||||||||| ||||| |||||||| || || ||||||||
cgctatcagttatcatatattcctgattttcgacctttaaagtagtcttcatgttta-tggttatgagatataatcagttttcctt--tccctatcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG

upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 18
tctacaattctaccataaaccagccttcctatgtgtagaacaatctctattttcaatggttttgagtcatttatgggttcct------ttgttcataatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG
|| |  || ||  ||   |  |  |||   |  | |  |  ||| ||| |    |||  |||    |  || |||| || ||      ||  |  |  |  ||||||| ||  |  | |||||||||||| |||| |||||||||   || || ||||||||||| |||||||||||
tccaatatcctttca---atta--cttatcaattctcaattaat-tctttggggaataatttcccttgtttcatggatttctagttaattaatttttgtacctcagGTCAAAGAATTAGCTGAAAAGGCACGAGCAGGGAAGCTTAAGCCCAATGAATTTCAAGGAGGAACTTTCAG
















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|71433813|gb|DR814863.1|DR814863
EST:     CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|61119124|gb|DN560085.1|DN560085
EST:     CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|211174833|gb|FL413958.1|FL413958
EST:     CAATAATAAGGAATGCTGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|76924990|gb|DV170231.1|DV170231
EST:     AATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: AATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|60347222|gb|DN214195.1|DN214195
EST:     CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|149003161|gb|EE038899.2|EE038899
EST:     CAATAATAAGGAAGGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|47961688|gb|CN844397.1|CN844397
EST:     GGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: GGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|50331519|gb|CO526645.1|CO526645
EST:     CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|37398003|gb|CF636310.1|CF636310
EST:     CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|40337298|gb|CK371368.1|CK371368
EST:     CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|50331482|gb|CO526608.1|CO526608
EST:     CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: CAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
EST: gi|88758153|gb|DY542294.1|DY542294
EST:     AATAATAAGAAATGGGGATCAAAAGACTATATTTGCAATATCCGCAGAG                         GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA
genomic: AATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 113

GGCCTGATGACCCCAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 151

GGCCTGATGACCCCAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

GGCCTGATGACCCCAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GGCCTGATGACCCCAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaataat ... aatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattttcaatggttttgagtcatttatgggttcctttgttcataatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG
                     tcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctacaattctaccataaaccagccttcctatgtgtagaacaatctctattttcaatggttttgagtcatttatgggttcctttgttcataatcactcagGTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - -aaccagc
- - - - - - - - - - - - - - ctatgtg