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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacagcaaaagtggttagtaggtgattacttgtatgttgagaccttggaccctttttctaattatgggagcttctttcttttcaaatgctatatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG

Basic information

species Zea mays
transcript GRMZM2G134889_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134889_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g01010.1 (Oryza sativa), 3'ss of exon 2
--aacagcaaaagtggttagtaggtgattacttgtatgttgagaccttggaccctttttcta-----attatgggagcttct-ttcttttcaaatgcta-tatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG
  | |  |     |  |        |   ||    ||| |       |  |  |||  |  |     | |||      |  | |||||||||||  ||| ||  || |||||||||||||||||||| ||||||||||||||||||||||||||   ||||||||||| |||||||| | |||||||||||| |||||||| ||  | |
gtaccttctcttctcttctactcaagtcaaccccgatgctct--ttctaaattcttactgcacacacactattattattaatcttcttttcaaaccctactacttacagGGTGCTCACAGTGATGAGATTGCTGCTGCTTCGAGGCTGGAAGATGCTATCAACTTTTACCAGACTTCCAATCCTGATGTTGCCAAGCTTTTTCACCTTG

upper sequence: GRMZM2G134889_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 2
---aacagcaaaagtggttagtaggtgattacttgtatgttgagaccttggaccctttttctaattatgggagcttctttcttttcaaatgctatatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG
   ||   |   | |   |  ||||      ||   ||  |   |  |  ||   | ||  |  |||||     || ||| | ||   ||||   || |  ||||| || | ||||| ||||||||||||||||| ||||| || |||    |||| |||||||| |||  || ||||||||| || |||||||||||||| |
ttgaatctctggattaaattataggcttgagctgtaatacttgaatgtatgaaattgttggtttttatgc---tttatttatcttgtgatgcataatgtgcagGGTCCTGAGAGTGAGGAGCTTGCTGCTGCTTCAAGGCTTGAGGATGATGTCAATTTTTATCAAACTGTGAATCCTGATGTGGCAAAGCTTTTCCATATTG
















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|78105579|gb|DV523997.1|DV523997
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
EST: gi|76923366|gb|DV169451.1|DV169451
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
EST: gi|148974381|gb|EE025158.2|EE025158
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
EST: gi|91872330|gb|EB402287.1|EB402287
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCNTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
EST: gi|71767698|gb|DR965635.1|DR965635
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGC
EST: gi|19057888|gb|BM736555.1|BM736555
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
EST: gi|149077067|gb|EE165723.2|EE165723
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTG
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTG
EST: gi|148967607|gb|EE018861.2|EE018861
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
EST: gi|148945960|gb|EC891253.2|EC891253
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCT
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCT
EST: gi|149099037|gb|EE185056.2|EE185056
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
EST: gi|19855080|gb|BQ060132.1|BQ060132
EST:     TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCC                         GGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC
genomic: TACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATC

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: 245

GCTCGGCCCAGCCGTGCAAAATGTCACCAGCGTCGACGAGGCCCAGAGCATACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

GCTCGGCCCAGCCGTGCAAAATGTCACCAGCGTCGACGAGGCCCAGAGCATACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 373

GCTCGGCCCAGCCGTGCAAAATGTCACCAGCGTCGACGAGGCCCAGAGCATACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 237

GCTCGGCCCAGCCGTGCAAAATGTCACCAGCGTCGACGAGGCCCAGAGCATACTCACCGGAGATGACAAAGCCGTCCTTGCCTTCCTCGACACACTATCCgtatgaacga ... atatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaccctttttctaattatgggagcttctttcttttcaaatgctatatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG
          ttctaat  putative branch site (score: 237)
                                 ttttcaaatgctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacagcaaaagtggttagtaggtgattacttgtatgttgagaccttggaccctttttctaattatgggagcttctttcttttcaaatgctatatatatagGGTGCTCACAGTGATGAGCTTGCTGCTGCTTCGAGGCTGGAAGATAGCATCAACTTTTATCAGACTTCGACTCCTGATGTTGCTAAGCTTTTCCATATCG

- cagcaaa
- - - - - - - - - - - - -ttacttg
- - - - - - - - - - - - - - - - -atgttga