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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttgctgtcatagcataacagtatcttcagattcatgccaaactatttttcttcatattgtttgataagttaaggtaatttgatacttcttttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG

Basic information

species Zea mays
transcript GRMZM2G460078_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460078_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 8
gtatgatttgctgtcatagcataacagtatcttcagattcatgccaaactatt---tttcttcatattgtttgataagttaaggtaatttgatacttcttttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG
||| | ||   || ||||   |    || | || ||||| |||| ||||||||   | || | | |||| | ||    ||| ||| ||| ||||||| |    |  ||||||||||| ||||| ||||| ||  |||||||||||||| ||||||||||||| ||| |||| || ||||| |  |||||||||||  ||||| |||||
gtacggttctatgccatatatttttggt-tttttagatttatgctaaactattacctgtccttaaattgctcgaggcattatggttattcgatacttttggactaccagGTTCCAACAATGTACACACGGCTATTGCAAGGGTATGATGGTATGGATCCTGAACAACAGTCTGCATCTTCCTTTGCTGCAAAGCAATTGAGGCTAATG
















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|14529467|gb|BI096600.1|BI096600
EST:     ATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGA                         GTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCT
genomic: ATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGAgtatgatttg ... tttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCT
EST: gi|78120378|gb|DV538762.1|DV538762
EST:     ATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGA                         GTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCT
genomic: ATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGAgtatgatttg ... tttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCT

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), 48 (downstream exon)
Score: 183

TATACCAAAATTCAGTGTAAGCGGGATATGGCAGAGATGGCGAGAATCATATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGAgtatgatttg ... tttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

TATACCAAAATTCAGTGTAAGCGGGATATGGCAGAGATGGCGAGAATCATATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGAgtatgatttg ... tttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 156

TATACCAAAATTCAGTGTAAGCGGGATATGGCAGAGATGGCGAGAATCATATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGAgtatgatttg ... tttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 967

TATACCAAAATTCAGTGTAAGCGGGATATGGCAGAGATGGCGAGAATCATATCCCAACGATGCGAGTAAAAGTACAGAGGCCATTACAGTATTTACTGGAgtatgatttg ... tttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttcatattgtttgataagttaaggtaatttgatacttcttttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG
                                atttgat  putative branch site (score: 967)
                                      tacttctttt  CT-rich tract
         atattgtttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatttgctgtcatagcataacagtatcttcagattcatgccaaactatttttcttcatattgtttgataagttaaggtaatttgatacttcttttatggcagGTTCCAACCATGTATACACGTCTGCTGCAAGGGTATGATAGTATGGATCCTGATCAAAAGTCGGCCTCTTCTTACGCTGCAAAGCATCTGAGGTTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG