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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGATGGCTCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttgctcctaatattacatatttattatcaagaatcgttcgccgtttatgatcttcctgtttttcag

Basic information

species Zea mays
transcript GRMZM2G135444_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135444_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 5'ss of exon 3
CTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGATGGCTCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttgctcctaatattacatatttattatcaagaatcgttcgccgtttatgatcttcctgtttttcag
| |||||||| || ||||||||||||||||||||||||||||| ||||| ||| | |||  ||| |||||||||||||||||||||||||||| ||||||||| |||||||  ||    ||| || | |||| | ||  | |   |    ||||  |  | |   ||||||||
CGGTAGCATCAGTTGGTGATTCACGTTGCATACTAGAATCTGCTGATGGTTCATTATACCATTTGTCAGCTGATCATCGCTTTGACTCCAACCAAGATGAgtaagttttgc--ctgccttta-atgtgtatttttaaagaactgccaatatttacaacatactcttttttcag
















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|148946428|gb|EC891737.2|EC891737
EST:     TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGA                         GGTCAAGCGCG
genomic: TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCG
EST: gi|149095947|gb|EE181613.2|EE181613
EST:     TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGA                         GGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
genomic: TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
EST: gi|148940139|gb|EC884892.2|EC884892
EST:     TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGA                         GGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
genomic: TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
EST: gi|149101338|gb|EE187455.2|EE187455
EST:     TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGA                         GGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
genomic: TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
EST: gi|149096893|gb|EE182691.2|EE182691
EST:     TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGA                         GGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
genomic: TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGT
EST: gi|149083526|gb|EE172858.2|EE172858
EST:     TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGA                         GGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATT
genomic: TCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATT

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: 43 (upstream exon), 49 (downstream exon)
Score: 3

CTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGATGGCTCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGTCGGTGGACCAGAG


Block sizes: 9 (upstream exon), 47 (downstream exon)
Score: 4

CTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGATGGCTCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGTCGGTGGACCAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 10

CTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGATGGCTCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGTCGGTGGACCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 384

CTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGATGGCTCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttg ... tgtttttcagGGTCAAGCGCGTGACAGCATGTGGGAGCAAAGTTGGGAAAATGGATATTGTCGGTGGACCAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGATGGCTCAATCTACTTTTTATCAGCTGATCATCGCTTTGACTCCAACCCAGATGAgtaggttttgctcctaatattacatatttattatcaagaatcgttcgccgtttatgatcttcctgtttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG