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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagctatcaggatccaaactgaccgagaactgtttgatatttttcttttacttgtttcattgatgcagttttatgccattctcaattttttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG

Basic information

species Zea mays
transcript GRMZM5G877316_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G877316_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 3
atagctatcaggatccaaactgacc-gagaactgtttgatatttttcttttacttgtttcattgatgcagttttatgccattctca-----attttttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG
|||  |||  | |   |||||  |  |   ||  |   |||  | | |||||||||| |  || || | ||   || | ||||| |     |  |||   |  |||||||| || ||||||||||| ||||| || || ||||||||||||||||||||||||||||||||||||
atatttatatgta---aaactatcttgccgaccttcacatacatatgttttacttgtat--tttatcctgtgcaat-caattcttataaagacctttcactgacagGAACTTGTTGCCAAAAGTATCGAGTCCTCGGATCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG

upper sequence: GRMZM5G877316_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 3
-atagctatcaggatccaaactga---ccgagaactgtttgatatttttcttttact-----tgtttcattgatgcagttttatgcc--attctcaattttttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG
  ||    |  || | ||   ||    |    |  ||||| || ||| | ||  |       ||| ||  || |  | |  |||  |  ||| |  | ||| ||    ||||||||  | || || |||||||| ||||| ||||| ||||| ||| | |||||||||||||||||||| 
ggtaatgttacggttgcattttgcagcctttcatttgtttaatgtttgttttgcatccacactgtctctctggtttattcatataactgattttgtaatttgtgcctgcaGGAACTTATTGCTAAGAGTATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA-

upper sequence: GRMZM5G877316_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 4
atagctatcaggatccaaactgaccgagaactgtttgatatttt-tcttttac-ttgtttcattgatgcagttttatgccattctcaattttttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG
            ||     |||     ||| |  |  || |||| | ||| || || |    ||| ||||| |  ||        |||||| |   | | |||||||  |||| ||||| ||||| ||||| ||||| ||||||||  | |||||||||||||||||||||
---------gtaatttttcctgtgtctgaaatcctatatgttttgtgtttcaccttatcattttggtgcagcta-atatgg----caatttctaaatgc-agGAACTTATCGCTAAAAGCATTGAATCTTCAGACCTTAACTTCTCTAGATACGGTGACACCTTTTTTGAG

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|18662176|gb|BM501785.1|BM501785
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATC----T--G------                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|78108789|gb|DV527206.1|DV527206
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATC----T--G------                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|76912266|gb|DV164646.1|DV164646
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATC----T--G------                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|61117466|gb|DN558427.1|DN558427
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATC----T--G------                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|71428140|gb|DR809190.1|DR809190
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATC----T--G------                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|19436862|gb|BM953272.1|BM953272
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCT                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|19057519|gb|BM736186.1|BM736186
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCT                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|87153853|gb|DY398642.1|DY398642
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATC----T--G------                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|19057686|gb|BM736353.1|BM736353
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCT                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|19436861|gb|BM953271.1|BM953271
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCT                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
EST: gi|78084825|gb|DV513218.1|DV513218
EST:     CAATTGTCCAGATTTATCTGGATAATGGTGGAGATC----T--G------                         GAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC
genomic: CAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTAC

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 3

CCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 10

CCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 13

CCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGAGATCTGGTTAGGCCTTCTgtgggtgtac ... ttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttacttgtttcattgatgcagttttatgccattctcaattttttgttaccagGAACTCGTCGCCAAAAGTATTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG
             cattgat  putative branch site (score: 13)
                                         ttttttgtt  putative PPT
                                 attctcaatttttt  TA-rich tract