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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttctttcttctctgtgccttatgcctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG

Basic information

species Zea mays
transcript GRMZM2G112672_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 4
---ttctttctttcttctctgtgccttatgcctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG
      | | ||    |  | |   || ||  |   ||  | || | ||   | |||| | |||    || ||||        | |||| | ||||||||||||||| ||||| || |||||||||||||||||||| |||||||||||||| |||
ttagcatatgttatgccctttttttttctgtgtctcttgcttttatcttcaatgttgtgtgtgaa---aagaaattcttgcattaactcaataatccttgcagTTTCTTTCCAGCTATATGACCTCAAGCAACAAGGGTTCATTGAAAGACAAGAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------------------------ttctttctttcttctctgtgccttatgc-ctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG
                                                                                                |  ||| |||  | |||||   ||||    | | ||| ||  ||| || ||  |     ||            || ||     ||||| |  |  ||||||||||||||||| | ||||| ||||| |||||||| || |||||||||||||||
gtaagaatgacaaatgtttagaagactttagctatctggtctactgttttatctgggttttgaatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatttccttaatgcatttgttattgatagtaatgcatatgttggggattcc---caactcttcc-tttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGGAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------------------------ttctttctttcttctctgtgccttatgc-ctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG
                                                                                                   | |||  | |||||   ||||    | | ||| ||  ||  || ||  |     ||            ||   |||  ||| | |  |  ||||||||||||||||| | ||||| ||||| || ||||| || |||||||| ||||||
gtaagaatgacaaatgtttagaagactttagctatgtggtctacttttttatctgggttttgaataggaagagcatttattggagagggagctagatcatgttttgtttctgtagtttatttatttccttaatgcattagttattaatagtaatgcatatgttgggcat---ttccaacttttct-tttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------------------------------------ttctttctttcttctctgtgccttatgcctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG
                                                                                               || |  ||||  | |      |||||       ||  || |  |||  |  |  |  ||   |    |   |     | |  | || |      ||||||||||||| ||||| ||||| || ||||||||||| ||||||||||||||||||
gtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatgatttcatgctgatgcttattgatgtatgtttgggatgccaaatc-atttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG

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|5846848|gb|AI999931.1|AI999931
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211265415|gb|FL346370.1|FL346370
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|31360067|gb|CD444424.1|CD444424
EST:     CAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: CAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|60354409|gb|DN221382.1|DN221382
EST:     GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|6194508|gb|AW146612.1|AW146612
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|78021323|gb|DV489710.1|DV489710
EST:     TGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: TGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211071789|gb|FK958795.1|FK958795
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|9952360|gb|BE638943.1|BE638943
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211483288|gb|FL326631.1|FL326631
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGARAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
EST: gi|211071790|gb|FK958796.1|FK958796
EST:     GGCGCTCTCAGTATTTCATCCCAACGCTCCCTTGGATGAGAAGATTGAGT                         TTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG
genomic: GGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGG

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), 46 (downstream exon)
Score: 114

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 173

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGAAGATCGAGTgtaagtttgt ... atccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG
                                ttctgac  putative branch site (score: 182)
                                              tccttgc  putative PPT
                    aaaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttctttcttctctgtgccttatgcctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA