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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtaaaggatccatcatttttttccattttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG

Basic information

species Zea mays
transcript GRMZM2G035150_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g64219.3 (Oryza sativa), 3'ss of exon 4
gt-ttgtgtaaaggatccatcatttttttccattttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG
|| ||   | ||  ||  |   ||||| || |||||            |||     |||| ||| ||   |||  |||  || |||||| |||||  |||| |||||||||||||| ||  ||||||| ||||||||||| ||||| ||| | ||||| |||
gtattacttcaaatatgtactctttttctctattttatg---------ctctacttatctcttt-tagcatgta-tcttatacacagTTCCGAGCATTGTCCGATCAATTTTACCGCACCACTGAACACCACAGATTTGTTCGGCAACAAATAGTGAAACAG
















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|74235678|gb|DT643592.1|DT643592
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|78092883|gb|DV521257.1|DV521257
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|71427954|gb|DR809004.1|DR809004
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGGTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|76289426|gb|DV028994.1|DV028994
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|71427953|gb|DR809003.1|DR809003
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|74235679|gb|DT643593.1|DT643593
EST:     GGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGGCA-CTGCCAG                         TTTCGAGCGCTGT
genomic: GGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGG-CAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGT
EST: gi|86466720|gb|DY233090.1|DY233090
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|71427180|gb|DR808230.1|DR808230
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|76291810|gb|DV031378.1|DV031378
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|78080763|gb|DV509175.1|DV509175
EST:     CTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: CTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
EST: gi|50327716|gb|CO522842.1|CO522842
EST:     TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAG                         TTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT
genomic: TGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTT

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: 45 (upstream exon), 49 (downstream exon)
Score: 62

GTTGGTGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 48

GTTGGTGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 73

GTTGGTGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 102

GTTGGTGGTGTACGGTTTGGTTGATCTCAAGGTTAAAGGAGATGGCAACTGCCAGgtttgtgtaa ... tcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG
              atctcac  putative branch site (score: 102)
                                           tctctt  putative PPT
                           tatttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgtaaaggatccatcatttttttccattttgcctgaagccatctcacagcatctatttgtattctgtggtctcttaaacagTTTCGAGCGCTGTCAGATCAATTTTACCGAACTCCTGAACATCACAGATTTGTCCGGCAGCAAGTGGTGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC