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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtgtgtgcacgcgcttaccccaacaggaagttaaaagcaatgctatccttgttacccatttttatactcatgtgtaacttcaaaattttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG

Basic information

species Zea mays
transcript GRMZM2G103047_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103047_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 3'ss of exon 4
--------------------tgtgtgtgtgcac-gcgcttaccccaacaggaagttaaaagcaatgctatccttgttacccat-ttttatactcatgtgtaacttcaaaatttta-aaca-cagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG
                    | | ||| | | | | |   ||  |||    ||  |||      || || |   | || | |  |  ||||  | ||  |    |  || || ||  | | ||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||| | |||||||| |||||||||||||| |||
gtaagggatatagctagctatttttgtcttcgctgtggaaactgcaaatataacataagcctgctgatagcagagctaacaaagtgctatatgcttgattcgtctgtaatttatatgatatcagGGCTGGATTTTGGAGTGCAATGGCCTCAAATGTCACCTTCCAGTCAAGGAATGTGTTGAGCAAGAAGCTTATGGTGAAGAAGGAG
















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|148999234|gb|EE036154.2|EE036154
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTNCA-GGA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGT-CAAGGA
EST: gi|60349997|gb|DN216970.1|DN216970
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|83279029|gb|DV943037.1|DV943037
EST:     TGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: TGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|149070711|gb|EE159127.2|EE159127
EST:     ATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|76916104|gb|DV166241.1|DV166241
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAA
EST: gi|74235578|gb|DT643492.1|DT643492
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|9794211|gb|BE552519.1|BE552519
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCA
EST: gi|60349346|gb|DN216319.1|DN216319
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|149072472|gb|EE160748.2|EE160748
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTTACTG                         GGCTGGATTTTG
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTG
EST: gi|91054476|gb|EB164894.1|EB164894
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|83278332|gb|DV942340.1|DV942340
EST:     GGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: GGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|76018096|gb|DT945266.1|DT945266
EST:     TGAGGCCTCCTTTAACTG                         GGCTGGATTGTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: TGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|74235577|gb|DT643491.1|DT643491
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|4753301|gb|AI657206.1|AI657206
EST:     ATTGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|78110415|gb|DV528827.1|DV528827
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
EST: gi|149007367|gb|EE040217.2|EE040217
EST:     ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG                         GGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA
genomic: ATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAA

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: 325

TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTGgtatacaata ... ttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatccttgttacccatttttatactcatgtgtaacttcaaaattttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG
                             gtgtaac  putative branch site (score: 438)
                                taacttcaaaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtgtgtgcacgcgcttaccccaacaggaagttaaaagcaatgctatccttgttacccatttttatactcatgtgtaacttcaaaattttaaacacagGGCTGGATTTTGGAGTGCAATGGCTTCAAATGTAACCTTCCAGTCAAGGAATGTGCTAAGCAAGAAACTTATGGTGAAGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - tgcacgc
- - - - - - - - - - -cccaaca
- - - - - - - - - - - - - - - - - - - -gcaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgt