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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagctgagtaactggcagtaaaacgaaacaagtatatggcatgtttctatttatatgtacagtactaatgttttttgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG

Basic information

species Zea mays
transcript GRMZM2G179459_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179459_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g32460.1 (Oryza sativa), 3'ss of exon 8
gtgaagctgagtaactggcagtaaaacgaaacaagtatatggcatgtttctatttatatgtacagtactaatgttttttgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG
|| ||  |||||||||| || ||   | || ||| ||||    || || |   | || || |  | ||     || ||  |||||||||   ||||||| |||||||| ||||| || |||||  |||| ||||||||||| |||||||| ||||||||||||
gttaacatgagtaactgacatta---ccaagcaattataccatattttacatgtcatgtgcattgaacc----ttcttgttgctgcagGCGGTGCATAACTTCAATGGTACCACAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG
















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|87155526|gb|DY400315.1|DY400315
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCCCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|110957807|gb|EE177859.1|EE177859
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|60337938|gb|DN204911.1|DN204911
EST:     TCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|18168054|gb|BM337894.1|BM337894
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|60351503|gb|DN218476.1|DN218476
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|33097796|gb|CF057756.1|CF057756
EST:     ACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: ACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|60340975|gb|DN207948.1|DN207948
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|213188152|gb|FM192776.1|FM192776
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|5566993|gb|AI881904.1|AI881904
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCCCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|149032716|gb|EE154942.2|EE154942
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
EST: gi|60344252|gb|DN211225.1|DN211225
EST:     TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAG                         GTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT
genomic: TCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 200

ATGTCCTCTGAGAAGCAAAGGAGAGAATCTGCACCACCTATCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

ATGTCCTCTGAGAAGCAAAGGAGAGAATCTGCACCACCTATCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG


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

ATGTCCTCTGAGAAGCAAAGGAGAGAATCTGCACCACCTATCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG


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

ATGTCCTCTGAGAAGCAAAGGAGAGAATCTGCACCACCTATCATATCTTCACATAAGCGTGCTGAGAAAGCTCAGTACTTCCTTGCTGAGgtgaagctga ... tgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatatggcatgtttctatttatatgtacagtactaatgttttttgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG
                                tactaat  putative branch site (score: 101)
                                      tgtttttt  CT-rich tract
          atgtttctatttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagctgagtaactggcagtaaaacgaaacaagtatatggcatgtttctatttatatgtacagtactaatgttttttgtgctgcagGTAATGCATAATTTCAATGGAACCACGGAGAAGGAACTGAGCTTAATTGTTGGCGATTATGTTGTTGTTCGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT