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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccgcgatccgttactgaattccccctgctccccccccccccccccccccccccccggcgcgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG

Basic information

species Zea mays
transcript GRMZM2G078458_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078458_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g03676.1 (Oryza sativa), 3'ss of exon 3
gtaagaccgcgatccgttactgaattccccctgctccccccccccccccccccccccccccggcgcgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG
                                                   | |   || |  | | |  |  |||| || | || | ||   ||||    | ||| | | |  |   || || |||||||||||||| |||||||| || |||||| ||||||| || || || |||||||| ||  |||||||||| ||  | ||||| || ||  ||
--------------------------------------------gtatggtcgcaatccacatctctccatgttaaacaacttgatcagtgattgaatt--ttggtaatttctct---agGTATTTGGATATGCTTCCAAGCACCTTCGGAAGCTCCATTTGGTTCACCGAAGATGAGCTTGCTGAGTTGGAAGGGACCACACTTCACCGGGCAACCGTG
















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|71447103|gb|DR828153.1|DR828153
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|94477458|gb|EB706416.1|EB706416
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|148953147|gb|EE152628.2|EE152628
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|149072634|gb|EE160863.2|EE160863
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|149112477|gb|EE295347.2|EE295347
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|91050911|gb|EB161329.1|EB161329
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|149079364|gb|EE168341.2|EE168341
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
EST: gi|76928343|gb|DV171591.1|DV171591
EST:     ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCC                         ATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA
genomic: ATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 89

GATGCCGCGCGCTCTTAGAGGACGGAGTCGTCGACGACCGCCTCCTCGTCATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 54

GATGCCGCGCGCTCTTAGAGGACGGAGTCGTCGACGACCGCCTCCTCGTCATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 56

GATGCCGCGCGCTCTTAGAGGACGGAGTCGTCGACGACCGCCTCCTCGTCATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 20

GATGCCGCGCGCTCTTAGAGGACGGAGTCGTCGACGACCGCCTCCTCGTCATGCTCTTCCTCATGGCCGAGCGCCGACGCCCTGGCTCACTCTGGAAGCCgtaagaccgc ... gcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG
     ttgtaaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccgcgatccgttactgaattccccctgctccccccccccccccccccccccccccggcgcgcgcttgtaaataattcgaaccgtagctgaagcggtgggtcactgcattcgcagATACTTGGATATGCTTCCGAGCACCTTTGGGAGCTCCCTTTGGTTTACTGAGGAAGAGCTTGCCGAACTGGAAGGGACAACTTTGCACCGAGCTACGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG