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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtacatgtacttcttatttatcaactgaggtttagaagtatatactgcctgctctgacctccgccctgcacgttctcatatactcaagttactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG

Basic information

species Zea mays
transcript GRMZM2G315931_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315931_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 3'ss of exon 16
----tgtacatgtacttcttatttatcaactgaggtttagaagtatatactgcctgctctgacctccgccctgcacgttctcatatactcaagttactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG
      | |  | |  |   | ||   || | |  ||    | ||  |     ||| | |  ||||   | |||||   |||||||| |  |||  || ||||||||||||||||||| |||||||| |||||||| |||| ||| || ||| | ||||| || || |||||||||||||| |||||||||||||| ||||| |
ctgaatttcgagaaactaaaacttccgaagtta--ttacttattaggttggatctgttttatcctct-tcttgcaccacctcatataattgagt-gctttgcagGTTGGACTACCCATCGCTGCTGGGGCATTGCTGCCAGTTACAGGTACGGTGCTGACCCCGTCGATAGCTGGAGCTCTAATGGGTTTTAGTTCTGTCGGCG
















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|211170369|gb|FL103278.1|FL103278
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTATATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|33094915|gb|CF054909.1|CF054909
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|78104271|gb|DV522689.1|DV522689
EST:     CATGAAGACGGTGAAGCAAAATCTTTGGGTGGCCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CATGAAGACGGTGAAGCAAAATCTTTGG-TGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|13249696|gb|BG360601.1|BG360601
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|12968157|gb|BG265104.1|BG265104
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|12968156|gb|BG265103.1|BG265103
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|211170365|gb|FL103274.1|FL103274
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|60397501|gb|DN230317.1|DN230317
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|211170368|gb|FL103277.1|FL103277
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA

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: 140

CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcctgctctgacctccgccctgcacgttctcatatactcaagttactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG
       ctctgac  putative branch site (score: 130)
                                            ttactct  putative PPT
                               tcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtacatgtacttcttatttatcaactgaggtttagaagtatatactgcctgctctgacctccgccctgcacgttctcatatactcaagttactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATACTGACACCATCAATAGCTGGAGCTCTGATGGGTTTTAGTTCGGTCGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT