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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccctgtttagatgcaaagtttttttagttttagaaaataccatggttttgtgtaatagttttgttttggcaaaccatgagttgtttgaatgtaa...

Basic information

species Zea mays
transcript GRMZM2G111713_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111713_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g45300.1 (Oryza sativa), 5'ss of exon 9
GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccctgtttagatgcaaagtttttttagttttagaaaataccatggttttgtgtaatagttttgttttggcaaaccatgagttgtttgaatgtaa
||||||||  ||||||||||||||||||||||||| || || |||||  |||||||||| |||||||| |||||        |   ||  |     | ||||    | ||| |      |   ||     || | || | |   |     ||| ||             
GTTAACACACTGATGGCACATGGAGACACATCATCTCTCCGTAAAATATTGACAGAGAGAATGCATTCGgtaagttttcaccttactgtgagtggatgttag----acaaacttttggaggcatgctatttattcttctctcttctttttatgggtgaag---------
















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|88758132|gb|DY542273.1|DY542273
EST:     ATGGAGACACATCATCGCTTCGGAAAATTTTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|76923556|gb|DV169545.1|DV169545
EST:     ATGGAGACACATCATCGTTTTGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|4827723|gb|AI668415.1|AI668415
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|50337822|gb|CO532948.1|CO532948
EST:     AGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: AGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|89251080|gb|DY622866.1|DY622866
EST:     AAATTCTGACAGAGAGGATGCATTCT                         TCTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: AAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|89248722|gb|DY620508.1|DY620508
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|71420007|gb|DR804974.1|DR804974
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         ACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
EST: gi|211237149|gb|FL440871.1|FL440871
EST:     ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCT                         CCTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC
genomic: ATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACAC

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), 49 (downstream exon)
Score: 137

GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 140

GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccct ... ttggctgaagACTATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAACACTTTGATGGCACATGGAGACACATCATCGCTTCGGAAAATTCTGACAGAGAGGATGCATTCTgtaaggccctgtttagatgcaaagtttttttagttttagaaaataccatggttttgtgtaatagttttgttttggcaaaccatgagttgtttgaatgtaa

- - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaata