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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcagaattatttgaatccagttggttttatttcaggtttggtgtagtgtctcactgttttatgtattatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA

Basic information

species Zea mays
transcript GRMZM2G086934_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086934_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 3'ss of exon 5
gtatgtcag-aattatttgaatccagt----tggttttatttcaggtttg---gtgtagtgt-ctcactgttttatgtattatactt-cagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA
||| | ||  | |  ||| | | ||||    || | || || |   ||||    |||||||| || |||  |||   ||   ||||| ||||| || |||| || ||||||||||||||||| || || ||||||||||| ||||||||||||||||| || || |||||||| || |||||||| |||||
gtaaggcaatagtgctttcagttcagtgatgtgttcttgttcctactttgtgaatgtagtgttctgactagttt---taccctacttgcagATGTTATTGGGGTTGTTCAGAGCGTATCTCCTACTCTTAGTGTTAGGAGGAAGATTGACAACGAGACGATTCCAAAGCGTGACATCGTTGTAGCGGATGA
















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|32944972|gb|CF049791.1|CF049791
EST:     TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAG                         ATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
genomic: TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
EST: gi|61118644|gb|DN559605.1|DN559605
EST:     TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAG                         ATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
genomic: TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
EST: gi|32825102|gb|CD964824.1|CD964824
EST:     TGTCAAGATTGATCAGCTAGGAC-ATACGTCGGTGGCAGGGAGCTTGTAG                         ATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
genomic: TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
EST: gi|32943914|gb|CF048733.1|CF048733
EST:     TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAG                         ATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
genomic: TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
EST: gi|18659482|gb|BM500361.1|BM500361
EST:     TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAG                         ATATTGTTGGTGTGGTTCAGACCGTATCTCCCACACTCAGTGTTAGGAGAA
genomic: TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
EST: gi|61118643|gb|DN559604.1|DN559604
EST:     TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAG                         ATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA
genomic: TGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAA

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: 312

GTTGAAGAAGCAGAGGGGGAGACTTTCCTTCCACCAGTGCAATACAACCTTGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTTGAAGAAGCAGAGGGGGAGACTTTCCTTCCACCAGTGCAATACAACCTTGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 45

GTTGAAGAAGCAGAGGGGGAGACTTTCCTTCCACCAGTGCAATACAACCTTGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA


Block sizes: 45 (upstream exon), 34 (downstream exon)
Score: 13

GTTGAAGAAGCAGAGGGGGAGACTTTCCTTCCACCAGTGCAATACAACCTTGTCAAGATTGATCAGCTAGGACCATACGTCGGTGGCAGGGAGCTTGTAGgtatgtcaga ... tatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttatttcaggtttggtgtagtgtctcactgttttatgtattatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA
                          gtctcac  putative branch site (score: 13)
                                   ttttatgtattatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcagaattatttgaatccagttggttttatttcaggtttggtgtagtgtctcactgttttatgtattatacttcagATATTGTTGGTGTGGTTCAGAGCGTATCTCCCACACTCAGTGTTAGGAGAAAGATTGACAACGAGACAATACCGAAGCGTGATATTGTTGTAGCAGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG