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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaaccaatcatttttatgtcagtttgtttttttccttcttcattggataattgtgctaagcatgtggatttgttgacctcaatagaagtcattt...

Basic information

species Zea mays
transcript GRMZM2G022061_T05
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022061_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g27840.1 (Oryza sativa), 5'ss of exon 11
------AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaacc-aatcatttttatgtcagtttgtttttttccttcttcattggataattgtgctaagcatgtggatttgttgacctcaatagaagtcattt--
      ||||||||||||||||||| |||||||||||||||||||| || || ||||| |||| | |||| |||      || || |||||||| || |||||||||||||| ||   ||||| | ||   |||  |   |    || ||   |||   |   | | |||  | ||      |  |||    | | | || |||     
TAGCAAAGAAACGAGAACAGGAACGCCAAAGGCAGGAAAAACTTGCGGAGGTAGGTCGGTACAGGGGTCGAAGC------AGGAGCCTTAGCCGATCTCCACCAAGgtaattgaattgaatcagtatt-catcacatcaatgcaatc-ttggacatgaaactgtagggctgtg-atagaatctgcttgcttcctaaataattcaagctg
















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|6918688|gb|AW400218.1|AW400218
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|93012252|gb|EB637772.1|EB637772
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|89250973|gb|DY622759.1|DY622759
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTTTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|67024598|gb|CO453347.1|CO453347
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|37385048|gb|CF629639.1|CF629639
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|113684467|gb|DW836849.1|DW836849
EST:     CCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|211251413|gb|FL479559.1|FL479559
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAAAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|40335728|gb|CK369798.1|CK369798
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|37388853|gb|CF631641.1|CF631641
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
EST: gi|94473364|gb|EB702322.1|EB702322
EST:     CGATACAAGCGTCGTAGCCGCAGTAGAAGTTTTAGCCGTTNNNNNNNAAG                         AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA
genomic: CGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTA

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), 48 (downstream exon)
Score: 79

AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 56

AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 85

AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 31

AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaac ... cctagcacagAAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaaccaatcatttttatgtcagtttgtttttttccttcttcattggataattgtgctaagcatgtggatttgttgacctcaatagaagtcattt

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