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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaactttctttgcaaaattgtaatctagtatactgatgcaatacatggtttatgaacattttgacacgaagtgttgttgcagggtctcacaacacatttcactgaatattcttcttttttgtcatgggctattcgtttcag

Basic information

species Zea mays
transcript GRMZM2G098679_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098679_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 13
ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttc----------aactttctttgcaaaattgtaatctagtatactg-atgcaatacatggtttatgaacattttgacacgaagtgttgttgcagggtctcacaacacatttcactgaatattcttct-tttttgtcatgggctattcgtttcag
|| ||||||  ||||||||| |||||||| ||||  |||||||||||||||| | |||||||||||||          ||        | |||| | | ||||  |  |||  ||||||||     | ||||     |       | | | |  |  |||| ||||      || | ||||||||||| |  | || || |  ||   |||| |||||||
ATCTCTTCTGCTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcctaccagtaaaaaagaaaagggaaaagtttcatctgttgcactatatgcaatattccatatatggcttatgaattttgcaatat-atcacagg-tctcttctgtcaatccactgaatattttcatattgttattgtgatttatttgtttcag
















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|37375628|gb|CF624264.1|CF624264
EST:     TGGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|211280254|gb|FL478194.1|FL478194
EST:     TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|148953878|gb|EC899256.2|EC899256
EST:     TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|60401580|gb|DN234387.1|DN234387
EST:     TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|211084269|gb|FL474824.1|FL474824
EST:     TGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTC
genomic: TGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATC-AAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTC

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), 37 (downstream exon)
Score: 17

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 599

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 612

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaactttctttgcaaaattgtaatctagtatactgatgcaatacatggtttatgaacattttgacacgaagtgttgttgcagggtctcacaacacatttcactgaatattcttcttttttgtcatgggctattcgtttcag

- - - - - - - - - - - - - - - - - - -  GCTGTT