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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctgtctgatccgttctcctccctttgtgtttctgctcccttgtgtgtttctgtgaaatttgtctgaacctgtttcggtttgtcgtttggtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 1
tcctgtctgatccgttctcctccctttgtgtttctgctcccttgtgtgtttctgtgaaatt-tgtctgaacctgtttcggtttgtcg---tttggtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG
   |||  | |   || || | |   | || | |   || |||  || | |  | ||| || | |||||   ||||| | ||| |     |||| | ||||||||||||||||||||||||||||| ||| ||||||||||||| |||||||||||||| ||||||
---tgttaggttt-ttgtcattctgatctgatccctgtcgcttccgtttatgcgggaacttctctctgattttgttttgtttttttttgttttgatttgagcagAGGACTCGCTGAAGCGGGAGTCCGGCACGAAGGTTCACCATGCCAACATCCAGGCCGCCAAG
















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|71438455|gb|DR819505.1|DR819505
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211175329|gb|FL101110.1|FL101110
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCTCGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211175332|gb|FL101113.1|FL101113
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211175327|gb|FL101108.1|FL101108
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCTCGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCT
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|71332448|gb|DR803183.1|DR803183
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|31354620|gb|CD438977.1|CD438977
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCTCGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|32798447|gb|CD950683.1|CD950683
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCTCGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211175325|gb|FL101106.1|FL101106
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCTCGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCTAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211175333|gb|FL101114.1|FL101114
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|71428865|gb|DR809915.1|DR809915
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|94478012|gb|EB706970.1|EB706970
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|71448421|gb|DR829471.1|DR829471
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211175328|gb|FL101109.1|FL101109
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|30306946|gb|CD001619.1|CD001619
EST:     CGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGGCCAAGGGGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATC
genomic: CGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCC-ACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATC
EST: gi|74244741|gb|DT652655.1|DT652655
EST:     CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC

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: 551

CCCTTCTCTCCTCTCCGCTCCCAATCTTATCGTCGCCTCCCTCGAAGTCGCCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 217

CCCTTCTCTCCTCTCCGCTCCCAATCTTATCGTCGCCTCCCTCGAAGTCGCCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 269

CCCTTCTCTCCTCTCCGCTCCCAATCTTATCGTCGCCTCCCTCGAAGTCGCCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

CCCTTCTCTCCTCTCCGCTCCCAATCTTATCGTCGCCTCCCTCGAAGTCGCCGCTGCCTTCATTCCACCATGGCGCTTCACGCCCCGGTCCACGTGATGAgtaagcggcc ... gtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttctgtgaaatttgtctgaacctgtttcggtttgtcgtttggtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG
         tgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctgtctgatccgttctcctccctttgtgtttctgctcccttgtgtgtttctgtgaaatttgtctgaacctgtttcggtttgtcgtttggtctgagcagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG

- - - ctgatcc
- - - - - - - - ctcctcc
- - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - -ctgctcc