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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcctacgcctacgcgacgcacggctccacgtccgtccgtctcgtcttagctaactgaccgcggtgccctgaacatgcgtacgtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC

Basic information

species Zea mays
transcript GRMZM2G096407_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096407_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g65660.1 (Oryza sativa), 3'ss of exon 2
gtacgcctacgcctacgcgacgcacggctccacgtccgtccgtctcgtcttagctaa-ctgaccgcggtgccctgaacatgcgtacgtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC
             ||| |  | ||    |   |   | ||    || | || | ||| |||| |||  ||||   || ||          |  ||||||| || |||||||||||||||||  ||||||||||||| ||||||||||||||||||||||| ||||| ||||| || ||||||||||||| 
--------gtaagtacact-cacattttttttctctcatctccatcttgttggttaaactgaacgcaatgccaaaaatat----------tttcagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGGGCACCATGGTCGGCTACACAATCACCGCAACCATAAGCATGGT
















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|50324689|gb|CO519815.1|CO519815
EST:     CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
EST: gi|148939591|gb|EC884211.2|EC884211
EST:     CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
EST: gi|74241093|gb|DT649007.1|DT649007
EST:     CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATTGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
EST: gi|148991824|gb|EE033411.2|EE033411
EST:     CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
EST: gi|76013340|gb|DT940510.1|DT940510
EST:     CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
EST: gi|101393258|gb|EB818560.1|EB818560
EST:     CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGG

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: 47 (upstream exon), 31 (downstream exon)
Score: 4

TACTACACCTCCACGCTGCTCGCCGGCGCCTACCGCGCGCCGCACCCCGTCACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 47

TACTACACCTCCACGCTGCTCGCCGGCGCCTACCGCGCGCCGCACCCCGTCACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 14

TACTACACCTCCACGCTGCTCGCCGGCGCCTACCGCGCGCCGCACCCCGTCACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 14

TACTACACCTCCACGCTGCTCGCCGGCGCCTACCGCGCGCCGCACCCCGTCACCGGCCACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcctac ... gtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtctcgtcttagctaactgaccgcggtgccctgaacatgcgtacgtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC
               aactgac  putative branch site (score: 14)