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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag

Basic information

species Zea mays
transcript GRMZM2G165357_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatca-tctatgtctgtag
| || |||||||| ||||| |||||||||||||| ||||| || |||||||| ||||||||||||||||||||||||||||| | ||                           ||| |||||  ||| |||||  ||||||   |   || || |  || |   | |  |||||||  || ||||| |||||||
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt--------------------------tagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtattttccaatctatctctgtag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA12G06980.3 (Glycine max), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcactt------aaacttcaatattagtagctca-----tagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag-
| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |||||  | | ||||||           | |  ||| | ||    || ||     |||   | ||        | |||||        || | |   | | |    |||||    | | | ||| |   
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCGgtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatatt----agtagctcatagccctctttgttatgtgata---actctgggcttatgattttttattaacagtatttatcatctatgtctgtag-----------------
| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||| || |||||  | | ||||||   ||   |||   |  |    |  | ||||| |           |     ||     | ||  ||  || |   | || | || ||  |       |||  | |                   
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCGgtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag
|||||||||| ||||||||||| || |||||||| || |||||  ||||||| ||||| |||||||| ||||| ||||||||   | ||| ||   || |  ||      | |        |  |||| |   ||   | |  |   |    || |  ||| ||  | | | | ||| |  |   | | |||||
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgcttcaac----tttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag
||||  |||| || ||||||||||| |||||||| || |||||  ||||||| || ||||| ||||| ||||| || ||||||  ||  | |||   ||    || |||  |        | |  | ||  ||  || |||    |       |||| || ||| || | | | |  |                
GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAGgtaac-ttttgtgtttttttt----tttaatcctga------acaaacttcaatga-atatgaagttttaatatgtatg-ttgtttctttatattttggacag-------------

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttca-tctttcacttaaacttcaatattagtagctcata-gccctctttgttatgtgataactctgggcttatgattttttat-taacagtatttatcatctatgtctgtag-------------------------------------------------------------------
| || |||||||| ||||||||||| ||||| || || || || |||||||| || ||||||||||||||||| || ||||| | |    ||  || ||   |     | |       | || |  ||| |     ||        | ||  |    ||||    | | ||| | | || |    ||    ||                                                                       
GAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAGgtaaaattgggctccctctctctgatccatacacccaacacacagacacccccacacctacacacattcactcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctgaaactctactttccaatgcactctcactttattttgaaatggtgatcctataacag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag
| || || || || ||||| ||||| |||||||| || ||||| || ||||| ||||| || |||||||||||| ||||||       ||   |  ||     |  |   ||  ||  | |   | ||||  | | |      |    || |  |||    | || ||  ||  |  |  || ||   |||   
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgta------tatacattcctcgtgttgtatcttttctaagttaacacgctctacgctttt-----atgtcggtccaatg----tgtactagaagcgtaaaatatttaaacctggc-

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|148939205|gb|EC883670.2|EC883670
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCC
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCC
EST: gi|149065532|gb|EE286652.2|EE286652
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|32838870|gb|CD978551.1|CD978551
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|13558126|gb|BG549482.1|BG549482
EST:     GAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|32850602|gb|CD990283.1|CD990283
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAGCACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|211264125|gb|FL402706.1|FL402706
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGAT
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGAT
EST: gi|211355257|gb|FL372995.1|FL372995
EST:     CGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTTG                         AAATCCGGAT-GCCCAGNATTTTCA-CACCTATGGGCCCTAG-ATGAACA
genomic: CGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATT-Ggtaacacttc ... atgtctgtagAAATCCGGATTGCC-AGGATTTTCAACACCTATGGGCC-TAGGATGAACA
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|71449953|gb|DR831003.1|DR831003
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|71449952|gb|DR831002.1|DR831002
EST:     AGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCA-TG                         A
genomic: AGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtag-
EST: gi|71449952|gb|DR831002.1|DR831002
EST:     AGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCA-TG                         A
genomic: AGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtag-
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|18173577|gb|BM348965.1|BM348965
EST:     AGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: AGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTNCA-CACCTATGGGCCTAGGATGAACATT
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTT-CAACACCTATGGGCCTAGGATGAACATT
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
EST: gi|45213764|gb|CK850000.1|CK850000
EST:     CGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG
genomic: CGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTG

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: 262

GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 589

GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 519

GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 986

GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttc ... atgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag

- - - - - - - - - - - - - - - - - - - - -  GCTGAT