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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatcatgctagttgtcatgtcaccggaaatagtggcagcaggcagccattattccatgaatactataccagttcgaggttgctcatttgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT

Basic information

species Zea mays
transcript GRMZM2G069827_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069827_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g01350.1 (Oryza sativa), 3'ss of exon 2
------tattatcatgctagttgtcatgtcaccggaaatagtggcagcaggcagccattattccatgaatactataccagttcgaggttgctcatttgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT
      || | |  |  || |    ||   ||    | ||| |       ||  | | |   | ||| | ||| |      |  | |||||   |||       |||||||| || || ||||||||| | |||||||| ||||| |||||||||||||| |  || ||||||||||||||||| || ||||||||||| 
gtactctactctactcttactcactattctactactagtagagt--atttgctactactccactatgca-actctgatgaatgtacgttgcctgttt-----caagGTACGAAGAACAGCGCAACATGCTCTACAACCAGACCTATAATCTCGACCAAGTCGCTTTCGCTGCCGATGGCCTCAAAGACGCTCAGCAGACC
















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|211462348|gb|FK983889.1|FK983889
EST:     AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAG                         GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
genomic: AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAGgcacgcgcca ... tgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
EST: gi|211462343|gb|FK983884.1|FK983884
EST:     AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAG                         GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
genomic: AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAGgcacgcgcca ... tgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
EST: gi|211462347|gb|FK983888.1|FK983888
EST:     AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAG                         GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
genomic: AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAGgcacgcgcca ... tgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
EST: gi|76915903|gb|DV166159.1|DV166159
EST:     AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAG                         GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
genomic: AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAGgcacgcgcca ... tgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
EST: gi|211462341|gb|FK983882.1|FK983882
EST:     AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAG                         GTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA
genomic: AGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAGgcacgcgcca ... tgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 6

GACGGTGGACGAGAAGATCAAGAAGCTGGACGAGGAGCTAGCCAGGTACAAGGAGCAGATCCGCAAGACCCGCCCCGGCCCGTCCCAGGAAGCCATCAAGgcacgcgcca ... tgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagccattattccatgaatactataccagttcgaggttgctcatttgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT
                                       ctcatttgcctctc  CT-rich tract
                aatactata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatcatgctagttgtcatgtcaccggaaatagtggcagcaggcagccattattccatgaatactataccagttcgaggttgctcatttgcctctcagGTACGAGGAGCAACGCAACATGTTGTACAACCAAACCTACAATCTCGACCAAGTTGGCTTTGCTGCCGATGGCCTCAAGGATGCTCAGCAGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG