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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgagctaacaagtataggtacctgaatgcttaacactaacttttttagcgcaaaaatcttccctggttttcataatgatgctgctgcttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG

Basic information

species Zea mays
transcript GRMZM2G353213_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G353213_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 10
aattgagctaacaagtataggtacctgaatgcttaacac-taacttttttagcgcaaaaatcttccctggttttcat--aatgatgctgctgcttatt----aacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG
        ||       |    || ||     |||   | | |  |   ||    | |||||||  |||| |||| |   |  |||||| || || |     |||||||| |||||||| | | |||||||||||||||||||||| ||||| |||||| | ||||| || ||||||||||||||||||||  ||||||||||||
-------ttatgtcccttgcagacttgcggtattattgcatgatgtaactaatatacaaatcttatctggctttccttagactatgctgatgtttttctctaaacagAAACAACATGGGTGGATCTCCTGATCAATGGGATAACCGAATGCTCGATCACTTGAAGAATTTTGACCTTAGCAGTCCAGAAGTCAGGCAGCAGTTTG
















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|32789084|gb|CD941320.1|CD941320
EST:     GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT                         AAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
EST: gi|32803778|gb|CD956014.1|CD956014
EST:     GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT                         AAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
EST: gi|32800822|gb|CD953058.1|CD953058
EST:     GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT                         AAATAACATGGGCGCAGCTCCTGATCAATGGGATAACCGCATACTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
EST: gi|32803516|gb|CD955752.1|CD955752
EST:     GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT                         AAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
EST: gi|32803636|gb|CD955872.1|CD955872
EST:     GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT                         AAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATG
genomic: GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATG
EST: gi|32803661|gb|CD955897.1|CD955897
EST:     GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT                         AAATAACATGGGCGCAACTCCTGATCAATGGGATAGCCGCATGCTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
EST: gi|32803435|gb|CD955671.1|CD955671
EST:     GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCT                         AAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA
genomic: GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCA

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: 48 (upstream exon), 18 (downstream exon)
Score: 66

GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG


Block sizes: 49 (upstream exon), 18 (downstream exon)
Score: 112

GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG


Block sizes: 47 (upstream exon), 18 (downstream exon)
Score: 32

GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG


Block sizes: 48 (upstream exon), 18 (downstream exon)
Score: 83

GGATGCTGCAGAATCCAATGTACCGCCAACAACTACAGGATATGCTgtaagtaata ... ttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagcgcaaaaatcttccctggttttcataatgatgctgctgcttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG
                        ttttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgagctaacaagtataggtacctgaatgcttaacactaacttttttagcgcaaaaatcttccctggttttcataatgatgctgctgcttattaacagAAATAACATGGGCGCAACTCCTGATCAATGGGATAACCGCATGCTTGATCACCTTAAGAACTTCGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - -tgaatgc
- - - - - - - - - - - - - - - - - aacacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgctg