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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtctacactaaccacaccaagtacactcacatgtttccatgattcaaccaaacgatccttgccatgatcttgtattcttgttggcttgttgctcatagtggccaatgaacttctacag

Basic information

species Zea mays
transcript GRMZM2G158818_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158818_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 5'ss of exon 6
CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtctaca-ctaaccacaccaagtacactcacatgtttccatgat-tcaaccaaacgatcc---ttgccat-gatcttgtattcttgtt---ggcttgttgctcata---gtggccaatgaacttctacag---------------------------------------------
||||||| |||||||| ||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||  | ||||||||||||||||||  || |  | | | ||||| ||   || ||||   | | |  || ||         |||    ||||||| |||| ||  |  || ||   |    ||  || | |    | |     | |    | ||                                              
CTATTGCACTCTCTGAGGATCACAAGCCAAATAGAAGCGATGAGAGGAAGCGAATTGAGAGTGCTGGTGGGGTTGTTATGTGGGCTGgtaagtcctgcttccatcaacacctagagtac-cacacaatactacaatatctgtgttctaatctgagttgccatagatcgtgcctgtttattttggagaagtcactgacatacataggtggaggagacttgcaaattgcgactatcatcttgctgatgatggtaaatggacttttgcag

upper sequence: GRMZM2G158818_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G08090.2 (Glycine max), 5'ss of exon 6
CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtctacactaaccacaccaagtacactcacatgtttccatgattcaaccaaacgatccttgccatgatcttgtattcttgttggcttgttgctcatagtggccaatgaacttctacag
| ||||| |||||||| ||||| ||||| || |||||||||||| ||||  |||| |||| |||||||||  | || |||||||| ||| || |  ||| ||     | ||  || | |  |||  ||| ||  |||    ||        |    |  |  ||    | | | |   ||   |  | | |||   |||           
CAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagat--acaatatttcaagcatata-aatagcatcattcaatagttctgttaa--------tattctatttctgc-cacatatag---tgcaacatacaatggg-gatgggtc-------

upper sequence: GRMZM2G158818_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G31890.1 (Glycine max), 5'ss of exon 7
CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtctacactaaccacaccaagtacactcacatgtttccatgattcaaccaaacgatccttgccatgatcttgtattcttgttggcttgttgctcatagtggccaatgaacttctacag
| | ||| |||||||| ||||| || || || |||||||||||| ||||  ||||||||| |||||||||  | || |||||||| ||| || |  ||| ||       ||  || | |  |||  ||  ||  |||         || ||         ||| |       || |  ||   |  | | |||   |||           
CAAATGCTCTCTCTGAGGATCATAAACCAAATAGAAGTGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagat--acaatatttcaggcatataaa-tagcatcatt--atagttctgttgtgatattctg--------cttctgccacatttag--tgcaacatacactggg-gatgggtc-------

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|20301082|gb|BQ164025.1|BQ164025
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|211312460|gb|FL459524.1|FL459524
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAATTATGTGGGCTG                         GAACTTGRAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|149098862|gb|EE184875.2|EE184875
EST:     GAATAGTTATGTGGGCT-                         GAACTTGGAGGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAAC
genomic: GAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGA-GGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAAC
EST: gi|211050684|gb|FL481891.1|FL481891
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAATTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|211342700|gb|FL234317.1|FL234317
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAATTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|211331038|gb|FL445937.1|FL445937
EST:     GAGAGTGCGGGTGGATTAATTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: GAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|9733204|gb|BE511956.1|BE511956
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|101388859|gb|EB816411.1|EB816411
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|19058198|gb|BM736865.1|BM736865
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|211345077|gb|FL234318.1|FL234318
EST:     TGATGAGAGGAAACSAATCGAGAGTGCTGGTGGAATAATTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|20300882|gb|BQ163825.1|BQ163825
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|211342699|gb|FL234316.1|FL234316
EST:     TTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
EST: gi|61119350|gb|DN560311.1|DN560311
EST:     TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAATTATGTGGGCTG                         GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACC

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: 112

CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 68

CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 86

CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 56

CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTGgtaaggtctacactaaccacaccaagtacactcacatgtttccatgattcaaccaaacgatccttgccatgatcttgtattcttgttggcttgttgctcatagtggccaatgaacttctacag

- - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA