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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactatggctgttctgttctgatatgtacggaacctgtgattcgcttataaattttcggctcaaactcttactgtcggtcgtatctttggtcgtacttttcagATGCTGAAGAATGCAAGCATCGAAGAG

Basic information

species Zea mays
transcript GRMZM2G074173_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074173_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g43594.3 (Oryza sativa), 3'ss of exon 6
gtgagactatggctgttctgttctgatatgtacggaacctgtgattcgcttataaattttcggctcaaactcttactgtcggtcgtatctttggtcgtacttttcagATGCTGAAGAATGCAAGCATCGAAGAG
                       |  |||||  | ||| |||    |||| |  ||  ||  |  ||||    |  |||   | | |      ||  ||| |  ||||||||||||||||||||||| ||||||
----------------gtgagagtactatgttggaaacttgtatgacgctgaccaaacttatgtgcaaaggactcatgtt--ttgcact----gtactacatg-cagATGCTGAAGAATGCAAGCATTGAAGAG

upper sequence: GRMZM2G074173_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 6
gtgagactatggctgttctgttctgatatgtacggaacctgtgattcgcttataaattttcggctcaaactcttactgtcggtcgtatctttggtcgtacttttcagATGCTGAAGAATGCAAGCATCGAAGAG-------------------------------------------------------------------------
                       |  |||||  | ||| |||    |||| |  ||  ||  |  ||||    |  |||   | | |      ||  ||| |  ||||||||||||||||||||||| ||||||                                                                         
----------------gtgagagtactatgttggaaacttgtatgacgctgaccaaacttatgtgcaaaggactcatgtt--ttgcact----gtactacatg-cagATGCTGAAGAATGCAAGCATTGAAGAGGTAATGCAACTGATCCTAAAGGCATCTCTCATTTTATCAGGGAACTACACCTAAATAATATCACAATAAATAT
















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|50323709|gb|CO518835.1|CO518835
EST:     TATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCATCGAAGAG
genomic: TATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactat ... tacttttcagATGCTGAAGAATGCAAGCATCGAAGAG
EST: gi|50323708|gb|CO518834.1|CO518834
EST:     CTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCATCGAAGAG
genomic: CTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactat ... tacttttcagATGCTGAAGAATGCAAGCATCGAAGAG
EST: gi|71417762|gb|DR804204.1|DR804204
EST:     TATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCATCGAAGAG
genomic: TATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactat ... tacttttcagATGCTGAAGAATGCAAGCATCGAAGAG

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: 46 (upstream exon), 46 (downstream exon)
Score: 34

CAGGGTTGTTTACACGTTACCTAGTGGTGGAGGTTCAGATGACTCTAGCGTATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactat ... tacttttcagATGCTGAAGAATGCAAGCATCGAAGAG


Block sizes: 40 (upstream exon), 34 (downstream exon)
Score: 7

CAGGGTTGTTTACACGTTACCTAGTGGTGGAGGTTCAGATGACTCTAGCGTATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactat ... tacttttcagATGCTGAAGAATGCAAGCATCGAAGAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 7

CAGGGTTGTTTACACGTTACCTAGTGGTGGAGGTTCAGATGACTCTAGCGTATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactat ... tacttttcagATGCTGAAGAATGCAAGCATCGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

CAGGGTTGTTTACACGTTACCTAGTGGTGGAGGTTCAGATGACTCTAGCGTATCGTCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactat ... tacttttcagATGCTGAAGAATGCAAGCATCGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattttcggctcaaactcttactgtcggtcgtatctttggtcgtacttttcagATGCTGAAGAATGCAAGCATCGAAGAG
                 ctcttac  putative branch site (score: 114)
                                             tacttttc  putative PPT
                                 tatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactatggctgttctgttctgatatgtacggaacctgtgattcgcttataaattttcggctcaaactcttactgtcggtcgtatctttggtcgtacttttcagATGCTGAAGAATGCAAGCATCGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA