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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggacaatgccgtagtgacgaaataattttatacgggaaggagtatcacctatctaaccttggattttactcatttgatacctcatgttgctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 8
aggacaatgccgtagtgacgaaataattttatacgggaaggagtatcacctatctaaccttggatttta-ctcatttgatacctcatgttgctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG
  |  | |       | |   || | ||   | |   |     | ||   ||  |    |  | || ||  | || |||   ||  |  | || |  |||||||||||||||||||||||| ||||||||||| |||||||| ||||| ||||||||||||||||||||||||||||| || ||||| || ||||||||||
--gtaagtatttcttttattcaagatttgagtgccacacaacttctcggttaagtgtgttcagtttatagtttatctgacgtcttgttgtactatgctcagGACCTTGCTATTGATGCTACTACAACAGCAGGTGTTGACCTAGGTCAAGGTATGCGTGAAGTTGATATCAAGAAATATATCAAAGTGGAGAAGGTTCCTG
















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|71438455|gb|DR819505.1|DR819505
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|71332448|gb|DR803183.1|DR803183
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|31360791|gb|CD445148.1|CD445148
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|31354620|gb|CD438977.1|CD438977
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|33093522|gb|CF053516.1|CF053516
EST:     AATTCACTGGCCAGTTTGGTGATCTTATGGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|211175333|gb|FL101114.1|FL101114
EST:     GAGCTCCATTGGTACAAA-TTCACTGGGCAGTTTGGTGATCTTNAT-GCT                         GACCTTGCTATTGATGCTACA
genomic: GAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTT-ATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACA
EST: gi|71428865|gb|DR809915.1|DR809915
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|94478012|gb|EB706970.1|EB706970
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|32932045|gb|CF036857.1|CF036857
EST:     GGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: GGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|32930502|gb|CF035314.1|CF035314
EST:     GGTACGAAATTCACTGGCCAGTTTGGTGATCTTA-TGNCT                         GACCTTGCTATTGATGCTACANCAACAGCAGGCGTTGACCTTGGTCAGGG
genomic: GGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTG-CTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGG
EST: gi|32934453|gb|CF039265.1|CF039265
EST:     ACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: ACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|71448421|gb|DR829471.1|DR829471
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
EST: gi|74244741|gb|DT652655.1|DT652655
EST:     AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT                         GACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT
genomic: AGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGT

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), 49 (downstream exon)
Score: 162

GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG


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

GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 45

GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 68

GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCTgtaagcatct ... ctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacctatctaaccttggattttactcatttgatacctcatgttgctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG
                  attttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggacaatgccgtagtgacgaaataattttatacgggaaggagtatcacctatctaaccttggattttactcatttgatacctcatgttgctgtattcagGACCTTGCTATTGATGCTACAACAACAGCAGGCGTTGACCTTGGTCAGGGTATGCGTGAAGTTGATATCAAGAAATACATTAAAGTTGAAAAGGTTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - caatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttg