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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattaatattcttgaaagtctactttttgttattgaggatagataggagcactcgtacttgcttgtttcagctgctgattatttctacataccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA

Basic information

species Zea mays
transcript GRMZM2G106140_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g37120.1 (Oryza sativa), 3'ss of exon 13
atattaatattcttgaaagtctactttttgt-tattgaggatagataggagcactcg--tacttgcttgtttcagctgctgattatttctacataccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA
   | | ||  |     | |  ||| ||||  |  || | || | |     |||| |  | |||  |    | |  || |   ||| | | |||| || ||||||||||||||||| |   | ||| |  ||||||||| ||| |||||||| |||||||| ||||| |||||||||||   ||| ||| || ||||||||||
--gtaagtacacc----atttcactgtttgcatggtgtgcattgtttttttcacttgattgcttcatctacttatttgtttcatatctttgcatatcacgtagGTCTTTTGAGAACCATGGTTAATGAGTTGAAGCAGGGCAGGTGTATAACACCAAAGCTGACATTTATCCATGGAGGACGAGAAGATCCAGCATTGTTTGA
















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|60397316|gb|DN230132.1|DN230132
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|60341248|gb|DN208221.1|DN208221
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|94478603|gb|EB707561.1|EB707561
EST:     CTTTTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|84977630|gb|DW476052.1|DW476052
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|32835394|gb|CD975072.1|CD975072
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|5917393|gb|AW054184.1|AW054184
EST:     TGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: TGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|71314647|gb|DR793945.1|DR793945
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|71299985|gb|DR786056.1|DR786056
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|148946574|gb|EC887854.2|EC887854
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|116823383|gb|EC866904.1|EC866904
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
EST: gi|149070988|gb|EE159393.2|EE159393
EST:     CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACT                         GTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC
genomic: CTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCC

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: 48 (upstream exon), 39 (downstream exon)
Score: 18

AGCGAGAGCCCAATATTTCTTCTTGACACATTTACCAACCTTATCGTTTACTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 15

AGCGAGAGCCCAATATTTCTTCTTGACACATTTACCAACCTTATCGTTTACTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA


Block sizes: 45 (upstream exon), 41 (downstream exon)
Score: 11

AGCGAGAGCCCAATATTTCTTCTTGACACATTTACCAACCTTATCGTTTACTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 16

AGCGAGAGCCCAATATTTCTTCTTGACACATTTACCAACCTTATCGTTTACTATTCCTCAACTGCTGATCCTTCATTTCCTTTTCCTCCACCCCGTGACTgtaagtacat ... taccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggagcactcgtacttgcttgtttcagctgctgattatttctacataccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA
                            tgctgat  putative branch site (score: 16)
                                 attatttctacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattaatattcttgaaagtctactttttgttattgaggatagataggagcactcgtacttgcttgtttcagctgctgattatttctacataccatgtagGTCTTTTGAGAACAACAATCAATAAACTGAAGCAGGACAGATGTATAACCCCAAAGCTTACATTCATCCATGGAGGGGAAGATGATTCAACATTGTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - attcttg
- - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - ggagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctg