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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatataattttaaatcaggttggggtttttgaaatttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG

Basic information

species Zea mays
transcript GRMZM2G143817_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 2
gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatataattttaaatca--ggttggggtttttgaa-atttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG
||||||     |       |       |   |||  |||   | |   ||| ||  || || ||  |  ||  |||||      |||    |||        |||||||| || || ||   ||| |||||||| |||||||| || || || || |||||||||||||||||||||||||||||||| |||||  ||
gtaagtcttgttgaaatcaattgtgtgtttgaaagcatgcagagtattacaataagta-aacttgcagccattggttgaatcaattgtgtgtttgggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTG

upper sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G03630.1 (Glycine max), 3'ss of exon 3
----gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatat-aattttaaatcaggttggggtttttgaaatttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG
    |||| | || | |  | |   || | |  ||    | || || ||| || | |  | |  || |||| || |         || | |||||       | |||| |||||||||||||    | || || ||| ||||||||  ||||||||| |||||||||||||||||||||||||||||| |  ||||||||
gtaagtaattcaaggataatgtatgcaacaacaatc---tctgctttcttgcatattgaacaagaagtttatataaatgaattaattcttaaattct-----acagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG

upper sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G35990.1 (Glycine max), 3'ss of exon 3
----gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatataattttaaatcaggttggggtttttgaaatttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG
    |||| | || | |  | |   || | |  ||    | || || ||| || | || | |  |   | |   |  ||     || | |||||       | |||| |||||||||||||    | || || ||| |||||||   ||||||||| |||||||||||||||||||||||||||||| |  ||||||||
gtaagtaattcaaggataatgtatgcaactacaatc---tctgttttcttgcatattaaacaagaagcttatataaattaataattcttaaattct-----acagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG

upper sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g00510.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatataattttaaatcaggttggggtttttgaaatttct-ttgc-atagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG
                                                                           |   || || || |   ||      | |  ||  |      | | |  ||    |  ||  ||||       ||    |  |  ||| || | |||  | ||||| || ||||| |||  | |||| ||||||| |||||| |  || || ||||||||||||||||||||||||||||| ||  |  || |  ||
gtaagtgtaactgtgtaaatcccagaagcttctcttgagttcaccctgaagtctgtgtgcacacttttgtggatttccatgtaacttgtctagagtttgtaggggaaccttgaaaaattgcttcatggaacctacctttaccctgcatttacatactgcaaagttatattgttacagAGCCAGATATGGGGTCCAGCTGGAGAAGGGAGTATTTGAAAGGCGCACGGCAGATTTCTTGTGGATGATGATATTTGGAGCTCTGACATTGCTG

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|211206714|gb|FL036118.1|FL036118
EST:     TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGAT                         AGCAAGGTATGGTGTCATGTTTGAAAAGGGAGCATTTGATAAACGGACTGC
genomic: TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
EST: gi|6031375|gb|AW076232.1|AW076232
EST:     TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGAT                         AGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
genomic: TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
EST: gi|18176218|gb|BM351250.1|BM351250
EST:     TTCTTCCTGGGACC-TTTTCC-TAAACTTTGGTATTCGCCTTCTGATGAT                         AGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
genomic: TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
EST: gi|67017752|gb|CO446501.1|CO446501
EST:     TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGAT                         AGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
genomic: TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
EST: gi|211209280|gb|FL036120.1|FL036120
EST:     TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGAT                         AGCAAGGTATGGTGTCATGTTGGAAAGAGGGAGCATTTGATAAACGGACTG
genomic: TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAA-AGGGAGCATTTGATAAACGGACTG
EST: gi|211206713|gb|FL036117.1|FL036117
EST:     TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGAT                         AGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
genomic: TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
EST: gi|211209279|gb|FL036119.1|FL036119
EST:     TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGAT                         AGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC
genomic: TTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGC

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: 43 (upstream exon), 48 (downstream exon)
Score: 34

GTATGGAGGATATTTACAAGTTTCTTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 116

GTATGGAGGATATTTACAAGTTTCTTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG


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

GTATGGAGGATATTTACAAGTTTCTTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 80

GTATGGAGGATATTTACAAGTTTCTTCTTCCTGGGACCATTTTCCATAAACTTTGGTATTCGCCTTCTGATGATgtaagtgaaa ... ctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacagtatatataattttaaatcaggttggggtttttgaaatttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG
                                          tttctttgc  CT-rich tract
      tatatataattttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatataattttaaatcaggttggggtttttgaaatttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT