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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaaataattgtgcactcatttcctccccacaatgttggttttcctttttcctctccccctctcttgttgtttgctcattctgggtttcaactc...

Basic information

species Zea mays
transcript GRMZM2G020096_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 13
GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaaataattgtgcactcatttcctcccca-caatgttggttttcctttttcctctccccctctcttgttgtttgct-cattctgggtttcaactc
||||||||| |||| |||||||||||| | ||||| ||||  |||||||| | ||| |||||| | ||||||||||| |||||||| |  |||||| ||  |  || |||||| |||  | ||| || |   || |    |    ||  |||         || ||||| |    | || ||     || |||  
GTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgagttatttgtgctctctgtccctgccaagttatataatatactgttgatccataaataaacttttgttttgccttacaatcaccagtttaac--

upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 13
GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaaataattgtgcactcatttcctccc------cacaatgttggttttcctttttcctctccccctctcttgttgtttgctcattctgggtttcaactc
||||||||| |||| |||||||||||| | ||||| ||||  |||||||| | ||| |||||| | || |||||||| |||||||| |  |||||| ||  |  || |||||| |||  | ||| ||       | ||| |    ||      |   |   |   | | |||   |    |||  |  | |||      
GTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACCTCTGATTGGACAAATGAAGAAAGAGAAATGCTAAGGCGAAAGgtatcttgagttatttgtgctctctgtccctgccaagttatataatatactgttgatccataaataaacttttgttttgccttacaatcacaccagtttt------
















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|26457119|gb|CA828702.1|CA828702
EST:     ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG                         GTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
genomic: ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
EST: gi|22543186|gb|BU093624.1|BU093624
EST:     ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG                         GTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
genomic: ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
EST: gi|89251366|gb|DY623152.1|DY623152
EST:     ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG                         GTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
genomic: ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
EST: gi|78544507|gb|DV622005.1|DV622005
EST:     ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG                         GTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
genomic: ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
EST: gi|91048671|gb|EB159089.1|EB159089
EST:     ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG                         GTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
genomic: ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
EST: gi|211306279|gb|FL001392.1|FL001392
EST:     ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG                         GTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
genomic: ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
EST: gi|60345665|gb|DN212638.1|DN212638
EST:     ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG                         GTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT
genomic: ACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGAT

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: 241

GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGATTTAGCCGAGGAAGTTCTAAAACTGGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 740

GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGATTTAGCCGAGGAAGTTCTAAAACTGGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2210

GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGATTTAGCCGAGGAAGTTCTAAAACTGGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaa ... tatcgattagGTACCGTTGACTGGTCTGAAGACACCATTTCGCGATGGATATGTTAGAGATTTAGCCGAGGAAGTTCTAAAACTGGCCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAGgtacctcaaaataattgtgcactcatttcctccccacaatgttggttttcctttttcctctccccctctcttgttgtttgctcattctgggtttcaactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccctc