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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacacttcagaatattaattaatttagctgtgtatgttatttaccttacgacaacttgaccccctttaacctttggggttcatccatgtctctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA

Basic information

species Zea mays
transcript AC177936.6_FGT008
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC177936.6_FGT008 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 16
gtgacacttcagaatattaattaatttagctgtgtatgttatttaccttacgacaacttgaccccctttaacctttggggttcatccatgtctctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA
                |||   |  ||  |   | |||   |  |  || ||   |||  ||    || |    ||    |  |||  | ||| |  |||||||| ||||||||  | |||||| | |||||||||||||||||||||||| |||| ||| |||||||||||||| | |||||||||||||||||||||||||
---------------gttagacatgttttcaacgcatgcattccattttgcgc--actccacaattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA

upper sequence: AC177936.6_FGT008 (Zea mays), 3'ss of exon 4
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
gtgacacttcagaatattaattaatttagctgtgtatgttatttaccttacgacaacttgaccccctttaacctttggggttcat--ccatgtctctcattt-------cagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA
          |||    ||||  |    | |  ||  |    || |     || || |||| |  | |  |   || |  |  |   |||||| | |  |||       ||||| || || ||  | |||||||||||| | |||||||| || || ||| | || ||| |||||||||| ||||||||||  |  ||||||||||| ||||
---------tagatagctaat-gacccggttaggt--ggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA

upper sequence: AC177936.6_FGT008 (Zea mays), 3'ss of exon 4
lower sequence: PP1S70_181V6.1 (Physcomitrella patens), 3'ss of exon 15
--------------------gtgacacttcagaatatta-attaattt-----agctgtgtatgttatttacc----ttacgacaacttgaccccc----tttaacctttggggttcatc-catgtc---tctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA
                     | |   | |||||| |   ||| | ||     ||   |  ||| | | ||      |||    || |            | |    ||||  ||| | | |||||    |   ||| ||||| || || ||  |||| ||||||||  | ||||||||||| |||||||| || |||||||||||||| ||  ||||||     || || ||||||||||
gtgaatatttcatacctcgaattattatccagaatttcggattcacttctgcaagtcatcgatgatgtgtagtgctgttattgaaattctgtatttcaagtgttttttttgttgttaaacgcatgtgatgttaaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTGATTGACCGGGAGTACCTTGAAAGGGACAAAGCCAATCCTCAGATCTACA

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|211342733|gb|FL007045.1|FL007045
EST:     CGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAG                         CTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAKAGAGCTTA
genomic: CGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAGgtgacacttc ... ctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTA
EST: gi|32939384|gb|CF044203.1|CF044203
EST:     CGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAG                         CTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTA
genomic: CGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAGgtgacacttc ... ctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTA

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: 184

GTTGATGCGGCCATAGTTCGAATAATGAAGACGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAGgtgacacttc ... ctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

GTTGATGCGGCCATAGTTCGAATAATGAAGACGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAGgtgacacttc ... ctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

GTTGATGCGGCCATAGTTCGAATAATGAAGACGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAGgtgacacttc ... ctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GTTGATGCGGCCATAGTTCGAATAATGAAGACGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAGgtgacacttc ... ctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgacaacttgaccccctttaacctttggggttcatccatgtctctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA
                 ctttaac  putative branch site (score: 131)
                                          tctctcatttc  putative PPT
                  tttaa  TA-rich tract