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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagttaccactctatatattcctctcagtcatttggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 6
gtaagagttaccact---ctatatattcctctcagtcatttggatgttaccattctaatttg---atgagtgt-------ggtaacaagttcctactcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG
||| || |||||| |   ||||  |||  |  || || ||    | | ||     |||| ||   ||   |||        | || ||  |  | ||     ||||||||||||||| ||||||||  |||||||||| ||||||||||| || ||||| |||||||||||||| |||||||| |||||||| |||||||||
gtaggatttaccattctcctatggattttttcca-tctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 7
-----gtaagagttaccactctatatattcctctcagtcatttggatgttac-cattctaatttgatgagtgtggtaacaagttcctactcctctca-agGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG
      ||| ||     | |   | | |   |   | |   || | | | |    || | |       | | |  | | |  |  || |||||  || |||||||||||||||||||  |||| |||||| |  | || ||   ||  |||||||||||||||||||| || |||||||||||||||||||| |||
ttctcttaaaagaagttatttcttttttattttgtatttgattcgttttcaagtcttttcacactggaattatcttcatatatatctgctccttacacagGTTGCATGTGCATTGCTTATGGCGGGTGAGGATCTAGACAAAAATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
------gtaagagttaccactctatatattcctctcagtcat-ttggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctca-agGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG
       |   | ||   | |  ||  |||      |||| | |   |    |  || ||| | || |   | |  | | | ||  || |||||  || |||||||||||||||||||  |||| |||||| |  | || |||  ||  |||||||||||||||||||| || |||||||||||||||||||| |||
atttcttttttattttatatttgattcattttcaatagtcttatcacactggaatatacta-tctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG

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|148986684|gb|EE030466.2|EE030466
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|60355786|gb|DN222759.1|DN222759
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|148995918|gb|EE035161.2|EE035161
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|149102315|gb|EE188183.2|EE188183
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|149081093|gb|EE170194.2|EE170194
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|148986685|gb|EE030467.2|EE030467
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|71437045|gb|DR818095.1|DR818095
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|148943253|gb|EC888314.2|EC888314
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGC
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGC
EST: gi|148943252|gb|EC888313.2|EC888313
EST:     TCAGTACAAGACAGCTTATTATTCATTTTCCCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: TCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|74235474|gb|DT643388.1|DT643388
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|111189546|gb|EE287682.1|EE287682
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT

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), 47 (downstream exon)
Score: 49

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG


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

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 13

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG
                            tggtaac  putative branch site (score: 153)
                                      ttcctactcctctc  putative PPT
          attctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagttaccactctatatattcctctcagtcatttggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC