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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctcaaattgtgctcgttattagtctgtggctgtgcaactcgtgcttaacaagtttggaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG

Basic information

species Zea mays
transcript GRMZM2G015989_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 12
gtttgtgctcaaa---ttgtgct----cgttattagtctgtggctgtgcaactcgtgcttaacaagtttg-gaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG
|||||| |||  |   |||| ||        || | | ||    | |||| ||||||  |||| | |||  |||| |||     ||||||| ||||||||||| |||||||||||||| |||||||| ||||||||  | |||||||| ||||||||||||||||| |||||||||||||||
gtttgtactctgacatttgttcttaagtacgatgaatatgcaattctgcagctcgtgtgtaacgaatttttgaacatgtatgatttcagGTCCTTGCCAATGATAACTTCAGGTATGGTTACAATGCCGCTACAGGAAAATATGAGGATTTGATGGCTGCTGGTATTATTGATCCCACCAAG

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------gtttgtgctcaaattgtgctcgttattagtctgtggctgtgcaactcgtgc-ttaacaagtttggaactt--gttgacatt------------cagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG
                                                  | ||   |||  || || |     ||| |   ||    |  || | ||   |  |  ||  |||| |||  | |||  ||             ||||  |  ||| ||| ||    |  ||||| |||||||| || || ||  | || ||||| ||||||||||||||||| ||||||||||| || 
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
















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|9254561|gb|BE345029.1|BE345029
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|32935512|gb|CF040324.1|CF040324
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|9952879|gb|BE639462.1|BE639462
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG

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: 384

TTACAAGGTTGGGGCTGAAATTGTAAGGAAGTCCTTGAGCTATCCACTTAAATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

TTACAAGGTTGGGGCTGAAATTGTAAGGAAGTCCTTGAGCTATCCACTTAAATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 362

TTACAAGGTTGGGGCTGAAATTGTAAGGAAGTCCTTGAGCTATCCACTTAAATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 443

TTACAAGGTTGGGGCTGAAATTGTAAGGAAGTCCTTGAGCTATCCACTTAAATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtctgtggctgtgcaactcgtgcttaacaagtttggaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG
                                          tgttgac  putative branch site (score: 443)
                         ttaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctcaaattgtgctcgttattagtctgtggctgtgcaactcgtgcttaacaagtttggaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT