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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggtatactgaaatccatttctcattaaagctgtgtatttgcactaacaagagtattcgatacttcaatttcccag

Basic information

species Zea mays
transcript GRMZM2G075153_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075153_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g25940.1 (Oryza sativa), 5'ss of exon 6
TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggtatactgaaatccat-ttctcattaaagctgtgtatttgcactaacaagagtattcgatacttcaatttcccag
||| ||||| || || || || ||||||||||||||| ||||| ||||||||||| ||||||| ||||| ||||| |||||||||||||| ||||||||||| |||   |  ||  || | | | | ||||||| |  | |  ||| ||  | |||||| ||||   |  || |         
TGATAGTACCTTTGCATCCCCAATCAATCAGAAGGCACTAACTCTAGGTGCTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgtttggaccaaacttcctgtactcattacacatatagatt-gccttgacaagaatattttgttttttag--------

upper sequence: GRMZM2G075153_T02 (Zea mays), 5'ss of exon 6
lower sequence: PP1S152_35V6.1 (Physcomitrella patens), 5'ss of exon 6
TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt-atactgaaatccatttctcattaaagctgtgtatttgcactaacaagagtattcgatacttcaatttcccag---------------------
|||  | ||||| ||| | ||| | |||||| |||  ||  |||| || || ||||| ||  |||| |||||||| |||||  | ||||||||||||||||||||||  | |   |  | |  ||||    |||    | | | |||  | |||  |   |||| | |     || |   | |                     
TGATGGGACTTTTGCGACTCCTGTAAATCAGCAGGTTTTGGCTTTGGGGGCCGACCTTGTACTTCACTCTGCAACAAAGTATCTCGCTGGACACAATGATgtgagttaatcaccttttattttattttatttta---ttttatttttttaataaataatctatt-gttgtgaaaaatgtgctgttaaggactaagctcccttat
















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|149094738|gb|EE180294.2|EE180294
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|211303407|gb|FL181618.1|FL181618
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|71419167|gb|DR804675.1|DR804675
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|61119178|gb|DN560139.1|DN560139
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|5343071|gb|AI795481.1|AI795481
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|148948278|gb|EC893795.2|EC893795
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTCCCAA-GTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|60398293|gb|DN231109.1|DN231109
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|149074757|gb|EE163186.2|EE163186
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|22133730|gb|BQ833872.1|BQ833872
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|78122335|gb|DV540719.1|DV540719
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|4647443|gb|AI622518.1|AI622518
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|76291941|gb|DV031509.1|DV031509
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|60355129|gb|DN222102.1|DN222102
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|74245809|gb|DT653723.1|DT653723
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|60397682|gb|DN230498.1|DN230498
EST:     ACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: ACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|47962545|gb|CN845254.1|CN845254
EST:     CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|32914041|gb|CF018853.1|CF018853
EST:     CTGACCTAGTTATTCATTCTGCATCGAAGTACATTGCTCGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: CTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
EST: gi|32849779|gb|CD989460.1|CD989460
EST:     TACATTGCTGGACACAATGAT                         GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT
genomic: TACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGT

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), 49 (downstream exon)
Score: 183

TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 301

TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 432

TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 153

TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggt ... aatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAGTACTTTCGCGTCACCTATCAATCAGAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCTGCAACGAAGTACATTGCTGGACACAATGATgtgagttggtatactgaaatccatttctcattaaagctgtgtatttgcactaacaagagtattcgatacttcaatttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA