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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttagactgaaacctatatgcgttgagtttgtctccattctgaagttacggaactgttttgctgtcatcaatcagacacattcatttcaagctttttttagtttttattaagttttggttctttattagtggatgctgactacatctacttcattccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG

Basic information

species Zea mays
transcript GRMZM2G158627_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158627_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 3'ss of exon 18
gtttgttagactgaaacctatatgcgttgagtttgtctccattctgaagttacggaactgttttgctgtcatcaatcagacacattcatttcaagctt--tttttagtttttattaagttttggttctttattagtggatgctgactacatctacttcattccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG
                                                                      ||||||    |      ||||    |||  | |||| ||| ||    |   || ||||| | |  ||  |  ||||    | |||||      ||  ||||||||||||| ||||| ||||||||||||||||||||||| ||||| ||| || ||||||||||||| || || ||||| ||||| ||
---------------------------------------------------------------------gatcaattcatcttcaatatttgccacttagtgtttattttataaatggacatgtttcttcagtgttgagtcttgacatactttactttccaatatacagTATGTCATGGAAGAAATGAATGTTAAGACTGTCACTCCATGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAG
















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|71432888|gb|DR813938.1|DR813938
EST:     TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG                         TATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCC
genomic: TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCC
EST: gi|22715593|gb|BU197851.1|BU197851
EST:     TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG                         TATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAAT
genomic: TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAAT
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG                         TATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCC
genomic: TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCC
EST: gi|20208226|gb|BQ134315.1|BQ134315
EST:     CAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG                         TATGTCATGGTAGGAAATCAATGTTAAGACTGACACTCCATGCAATGACCC
genomic: CAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGG-AGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCC
EST: gi|87156879|gb|DY401668.1|DY401668
EST:     TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG                         TATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCC
genomic: TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCC
EST: gi|26559569|gb|CA831804.1|CA831804
EST:     TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG                         TATGTCATGGAGGAAATCAATGTT
genomic: TGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 193

GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 82

GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 144

GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 63

GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAGgtttgttaga ... ttccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagttttggttctttattagtggatgctgactacatctacttcattccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG
                         tgctgac  putative branch site (score: 63)
                                        cttcattcc  putative PPT
          ttctttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttagactgaaacctatatgcgttgagtttgtctccattctgaagttacggaactgttttgctgtcatcaatcagacacattcatttcaagctttttttagtttttattaagttttggttctttattagtggatgctgactacatctacttcattccatgtagTATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA