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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaatattatcatgtttatttttgtatagtattgtttataattgcttcctgttaatggaatcatttgattttcag

Basic information

species Zea mays
transcript GRMZM2G164956_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164956_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os09g34910.1 (Oryza sativa), 5'ss of exon 9
TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaatattatcatgtttatttttgtatagtattgtttataattgcttcctgttaatgga-atcatttgattttcag
||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||||| |   |||    | |  | |||||||         || |||| || | | |||  |||   |  |  ||||||||||||
TGTGAACCTCCACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaattcggttac-tatattttttc-------tgcttatgatggttaccttctaagcaatgtgttttgattttcag
















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|22491136|gb|BU051059.1|BU051059
EST:     CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTG
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTG
EST: gi|32928427|gb|CF033239.1|CF033239
EST:     CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTA
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTA
EST: gi|32846981|gb|CD986662.1|CD986662
EST:     CCGTGACGTTGAAGCTTACACACACCGGTCAGGTCGGACAGGGGGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTA
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTA
EST: gi|19272557|gb|BM888813.1|BM888813
EST:     CCGAGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTG
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTG
EST: gi|32929175|gb|CF033987.1|CF033987
EST:     CCGAGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGT
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGT
EST: gi|161407373|gb|DW042376.1|DW042376
EST:     CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAA
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAA
EST: gi|87153206|gb|DY397995.1|DY397995
EST:     CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTG
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTG
EST: gi|32928455|gb|CF033267.1|CF033267
EST:     CCGTGACGTTGAAGCTTACATACACCGGTCGGGTCGGACAGGGAGAGCAG                         GTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTA
genomic: CCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTA

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: 471

TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTGTCAGCAGACTAGAAAGGGAATCTGGGGTTAAGTTCGAACATATCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 428

TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTGTCAGCAGACTAGAAAGGGAATCTGGGGTTAAGTTCGAACATATCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 460

TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTGTCAGCAGACTAGAAAGGGAATCTGGGGTTAAGTTCGAACATATCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaa ... tgattttcagGTAATACTGGTGTTGCTGTCATGCTTTATGAGCCCAGATATAAGTACAGTGTCAGCAGACTAGAAAGGGAATCTGGGGTTAAGTTCGAACATATCTCTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaatattatcatgtttatttttgtatagtattgtttataattgcttcctgttaatggaatcatttgattttcag

- - - - - - - - -  TTGAAG
- - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG