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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgttgattttcttgcttagttacaacatcatacatgtatattgacgtcaccattttctgtttagacagtaaatatcttctggatatgattcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA

Basic information

species Zea mays
transcript GRMZM2G077299_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g03470.3 (Oryza sativa), 3'ss of exon 13
tcgttgattttcttgcttagttacaacatcatacatgtatattgacgtcaccattttctgtttagacagtaaatatcttct---ggatatgattcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
| | | |||  |||   |  |||||      | | ||  |||| |  ||  |   | |   || | || ||||||| ||       ||||| ||    ||||||||||||| ||||| || |||||||||||| |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
ttgcttattcacttctatctttacaga--tgtgc-tgcctatttatctcttctcatccctattggccattaaatatatttcttcatatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA

upper sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 13
tcgttgattttcttgcttagttacaacat-catacatgtatattgacgtcaccattttctgtttagacagtaaatatcttctggatatgattcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
|| |   |  |  || |||  |         |  | || |   | |   || |  || ||  ||      ||  | |||||   ||||| ||    ||||||||||||| ||||| || |||||||||||| |||||||||||||||||||||| ||||||||||||||||| || |||||||||||||||||||||||||
tcatgtgtgatgatgtttacatgttttggataatcttggaacctcattgcatctcttgcttattcacttctatctttcttc-atatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGA
















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|32847594|gb|CD987275.1|CD987275
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGT
EST: gi|213170538|gb|FM181869.1|FM181869
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTACGTTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
EST: gi|116814377|gb|EC856917.1|EC856917
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
EST: gi|12045517|gb|BF727656.1|BF727656
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
EST: gi|32846175|gb|CD985856.1|CD985856
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGT
EST: gi|32865761|gb|CF005443.1|CF005443
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
EST: gi|32846927|gb|CD986608.1|CD986608
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTA
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTA
EST: gi|17970148|gb|BM276913.1|BM276913
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
EST: gi|32835529|gb|CD975207.1|CD975207
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGT
EST: gi|22489289|gb|BU049212.1|BU049212
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGT
EST: gi|32846588|gb|CD986269.1|CD986269
EST:     TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG                         GTTTTTGTAAGTGAGTA
genomic: TGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTA

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), 48 (downstream exon)
Score: 61

GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 39

GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 875

GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctg ... tcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtcaccattttctgtttagacagtaaatatcttctggatatgattcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
                        taaatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgttgattttcttgcttagttacaacatcatacatgtatattgacgtcaccattttctgtttagacagtaaatatcttctggatatgattcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA