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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttatataaatatttgcatgaagttatattatttattatttcaagtagagcttaaagtaacacatttgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA

Basic information

species Zea mays
transcript GRMZM2G000177_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000177_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 8
gtacttata-taaatatttgcatgaagttatattattt----attatttcaagtagagcttaa--agtaacacatttgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA
     |||| | | ||||| | ||   || |||| |||     |||||| | | ||||||||   |||| || || |  ||  ||||||||||| |||||||| ||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||
----gtatactcactatttccgtgtgattgtattttttttttgttatttaaggaagagcttatgcagtagcatatcttttgtgcagGAAATAAGACGCATTAAACCAGTACCTAAACTTGCTTGCCATAGTGTTGCATCGTGGTGTCATCCTCGTGCACCAAACCTTGATATTCTGACTTGTGTCA

upper sequence: GRMZM2G000177_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G41130.1 (Glycine max), 3'ss of exon 8
----------------------gtacttatataaatatttgcatgaagttatattatttattatttcaagtagagcttaaagtaacacatttgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA
                         ||  | ||||| ||||    || || |  |  | | ||     | |  ||| | ||  ||  | |||| | |||||||  |  |||| || |||||||| || ||| | ||||| || ||||| || || ||||| ||||| || || ||||||||||||||||||||||| ||||
gtgtggtagtggggctaatgcctggctattttaaatttttgtg-aaaattctcctggtaactagaaagactt-agcatgaa--aaagcttttgattctcagGAGCTGCGGCGTATAAAGCCAGTTCCCAAATTGGCTTGCCACAGTGTGGCTTCTTGGTGCCATCCTCGAGCTCCAAACCTTGATATTCTAACTTGCGTCA

upper sequence: GRMZM2G000177_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 8
-----gtacttatataaatatttgcatgaagttatattatttattatttca---------agtagagcttaaagtaacaca---tttgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA
     ||| |  |   |||  |||  |    | || || | |   | |||          || |   ||||  || | | |   |||| | | |||||  |  |||| || |||||||| || ||| | ||||| || ||||| || || ||||||||||| || || ||||||||||||||||||||||| ||||
gtgtggtagtggtgctaatgcttggctattttaattttttgtgaaaattctcctggtaatagaaagacttagtgtgaaaaagcttttgattcccagGAGCTGCGGCGTATAAAGCCAGTTCCCAAATTGGCTTGCCACAGTGTGGCTTCTTGGTGTCATCCTCGAGCTCCAAACCTTGATATTCTAACTTGCGTCA

upper sequence: GRMZM2G000177_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT5G24710.1 (Arabidopsis thaliana), 3'ss of exon 8
gtacttatataaatatttgcatgaagttatattatttatt--atttcaagtag-agcttaaagtaacacatttgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA
||| |  | ||  |   || ||| | || |  |||||     || |||  ||  | | |  |     || |||  |   |||||  || |  | ||||| || || || ||||| ||||| || ||||||||||| |||||||| || || || ||||||||||||||| | ||||| || |
gtaatggtgtatct-catgtatggatttttcatattttcccgatctcatttattaacatgcatatctacttttattctacagGAGCTACGTAGAATTAAACCTGTCCCGAAACTAGCTTGCCACAGTGTTGCATCTTGGTGTCACCCTCGAGCGCCAAACCTTGATATTTTGACTTGCGTTA

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|60346425|gb|DN213398.1|DN213398
EST:     CAATAGGGGCTGATAAAACTTTAGCCATATGGGATACTGTTACTTTCAAG                         GAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCA
genomic: CAATAGGGGCTGATAAAACTTTAGCCATATGGGATACTGTTACTTTCAAGgtacttatat ... tgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCA




















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: 299

AGTTGCAGTTGAACTTTCAAGGGTGATGGGGAGTGCTCCACAGCTCATTACAATAGGGGCTGATAAAACTTTAGCCATATGGGATACTGTTACTTTCAAGgtacttatat ... tgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

AGTTGCAGTTGAACTTTCAAGGGTGATGGGGAGTGCTCCACAGCTCATTACAATAGGGGCTGATAAAACTTTAGCCATATGGGATACTGTTACTTTCAAGgtacttatat ... tgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 122

AGTTGCAGTTGAACTTTCAAGGGTGATGGGGAGTGCTCCACAGCTCATTACAATAGGGGCTGATAAAACTTTAGCCATATGGGATACTGTTACTTTCAAGgtacttatat ... tgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

AGTTGCAGTTGAACTTTCAAGGGTGATGGGGAGTGCTCCACAGCTCATTACAATAGGGGCTGATAAAACTTTAGCCATATGGGATACTGTTACTTTCAAGgtacttatat ... tgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatattatttattatttcaagtagagcttaaagtaacacatttgctgctcagGAAATAAGGCGCATTAAGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCA
                                 aagtaac  putative branch site (score: 291)
     tattatttattatttc  TA-rich tract