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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagattttgcactcccagaaagagctgttctgctagatcttgatgtaatcagaacagttcaattgacaacatgtgcaattttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC

Basic information

species Zea mays
transcript GRMZM2G113202_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 17
gtgcagattttgcactcccagaaagagctgttctgctagatcttgatgtaatcagaacagttcaattgacaacatgtg--caattttttc---agGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC
  | |  ||||     |||  ||  |     | ||||||||| |||   ||  |||  ||||  |||||||   | ||  |||||||||    |||| ||| |||||||||||||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||||
--gtaattttttttggccccaaataa--caatttgctagatcatgaatgaagtagattagttttattgacagtgtctgtccaattttttttaaagGGACAATTGTTCCAACTTATGCAAAGACTCGAAAGTACAACACCACACTTTATACGTTGTATTAAGCCAAACAATTTGCAACTCCCTGCAATTTATGAAC

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 16
gtgcagattttgcactcccag---aaagagctgttctgctagatcttgatgtaatcagaac--agttcaattgacaac-atgtgcaatttt----ttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC
 | |   |||   |    ||    ||| |   ||| |   || |  |||| | ||        |||| |  | | ||  || | |  | ||    | ||||||||| |||||| ||| ||||||  ||| || ||||| || ||||| |||||||| ||||||||||| || ||| | |||   |||| |   ||||| |
tttcccctttactaaaagcaacttaaatattcgttttcacaggtagtgatattattgcgctttagttgatcttaaaatgatttcctctgttggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTTATTCGCTGCATTAAACCGAATAATCTCCAATCACCTGAATCATATGAGC

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 18
gtgcagattttgc----actcccagaaagagctgttctgctagatcttgatgtaatcagaac--agttca-attgacaacatgtgcaattttt----tcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC
 | |    | | |    |    |  ||| |    || |   || |  |||| | |||       |||| | ||| | |  || | |  | |||     ||||||||| |||| ||||| |||||| ||||||| ||||| || ||||| |||||||| ||||||||||| || ||| | |||   |||| |   ||||| |
-ttccccctctactaaaagcaacttaaatattctttttcacaggtagtgatattatcgcgctttagttgatattaaaatgatttcctctgtttgtgtccagGGTCAATTGTTTCAACTGATGCAACGACTGGAGAGTACTACTCCACATTTTATTCGCTGCATTAAACCCAATAATCTCCAATCACCTGAATCATATGAGC

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 17
--gtgcagatt----ttgcactcccagaaagagctgttctgctagatcttgat---gtaatcagaacagtt--caattgacaacatgtgcaattttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC
   || | |||    ||  |||  || |||         |  | ||  | | |   ||     ||   |||    | | |   | ||||    ||||| ||||||||||||||||||| |||||  | || || |  ||||| ||||| || |||||||||||||| || |||||||| ||   ||||| ||  ||||| |
gtttgtaaattagagttatactatcaaaaaatatctcagtaattgagttggtttctgtgccttgatatgttgcttactcatttcttgtgttggttttt-agGGTCAACTGTTCCAACTGATGCAGCGTCTTGAGACCACAACACCACATTTCATTCGTTGCATTAAGCCCAACAATTTTCAGTCTCCTGGAAACTATGACC

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|211295410|gb|FL097175.1|FL097175
EST:     GATCTAGNGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211293269|gb|FL097161.1|FL097161
EST:     NATCTAGNGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295412|gb|FL097177.1|FL097177
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211293267|gb|FL097159.1|FL097159
EST:     GATCTAGNGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295409|gb|FL097174.1|FL097174
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211293272|gb|FL097164.1|FL097164
EST:     GATCTAGNGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295415|gb|FL097180.1|FL097180
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295407|gb|FL097172.1|FL097172
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCAAGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|76924723|gb|DV170102.1|DV170102
EST:     TGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: TGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295413|gb|FL097178.1|FL097178
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295405|gb|FL097170.1|FL097170
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295414|gb|FL097179.1|FL097179
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211293265|gb|FL097157.1|FL097157
EST:     GATCTAGNGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211293274|gb|FL097166.1|FL097166
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|32934816|gb|CF039628.1|CF039628
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTAC
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTAC
EST: gi|211293264|gb|FL097156.1|FL097156
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|32932787|gb|CF037599.1|CF037599
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTA
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTA
EST: gi|211293273|gb|FL097165.1|FL097165
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTCTCCAA
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGT-TCCAA
EST: gi|211293266|gb|FL097158.1|FL097158
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|211295406|gb|FL097171.1|FL097171
EST:     GATCTAGNGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
EST: gi|32930639|gb|CF035451.1|CF035451
EST:     GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTA
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTA
EST: gi|32826955|gb|CD966633.1|CD966633
EST:     GATCTGGTGCTGCTGATTCTCAAAAGCTAAGTGTTGCCATGAAGTTCAAG                         GGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT
genomic: GATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTT

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: 145

TGCATCGAAGATGCTAGTTCAATCAGATAATTCTATGTCTGTTCCATATAGATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

TGCATCGAAGATGCTAGTTCAATCAGATAATTCTATGTCTGTTCCATATAGATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

TGCATCGAAGATGCTAGTTCAATCAGATAATTCTATGTCTGTTCCATATAGATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 77

TGCATCGAAGATGCTAGTTCAATCAGATAATTCTATGTCTGTTCCATATAGATCTAGTGCTGCTGATTCTCAAAAACTAAGTGTTGCCATGAAGTTCAAGgtgcagattt ... attttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagatcttgatgtaatcagaacagttcaattgacaacatgtgcaattttttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC
                            aattgac  putative branch site (score: 77)
                                              ttttttc  putative PPT
                                            aattttttca  TA-rich tract