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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaatgaatatgtaaattcttattcttgtagcgaatttgggaaatccttcaaatctgggtgttccgatcaattatcccatatattccttgcatag...

Basic information

species Zea mays
transcript GRMZM2G044819_T03
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g14810.1 (Oryza sativa), 5'ss of exon 14
AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgta-------cat-caatgaatatgtaaattcttattcttgtagcgaatttgggaaatccttcaaatctgggtgttcc-gatcaattatcccatatattccttgcatag
||||||| || ||||||||||||||||||||||||||||| |||||||||||||| || |  |||||||||||| |||||||||| || ||||||||||||||       ||| || | | |  |||| | || ||   | |   ||||    ||||    | ||||  |    |||  ||||  ||  || || ||||  |       
AGCTTACAGAAAGTATGCAAAAGTTGCTCATTGTTATGCAGAGATTAGATGAAAAAATTGCACCAATGCTAGAATCAGATGGAGAGCTGTTCAATAAAAGgtaaagcaggcatgcagtcattgcgtaattcctcatgtcttt---gaatgcaagaaacgtctgaaattcgtcgcttctagatctgttgccctatgtatttttg------

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 5'ss of exon 14
AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgta-------cat-caatgaatatgtaaattcttattcttgtagcgaatttgggaaatccttcaaatctgg-gtgttccgatcaattatcccatatattccttgcatag
||||||| || ||||||||||||||||||||||||||||| |||||||||||||| || |  |||||||||||| |||||||||| || ||||||||||||||       ||| || | | |  |||| | || ||   | |   ||||    ||||    | ||||  |  |  |   ||||  ||  || || ||||  |||||   
AGCTTACAGAAAGTATGCAAAAGTTGCTCATTGTTATGCAGAGATTAGATGAAAAAATTGCACCAATGCTAGAATCAGATGGAGAGCTGTTCAATAAAAGgtaaagcaggcatgcagtcattgcgtaattcctcatgtcttt---gaatgcaagaaacgtctgaaattcgtcgcttctagatctgttgccctatgtattt-ttgcag--

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA15G21240.1 (Glycine max), 5'ss of exon 13
AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacat-caatgaatatgtaaattcttattcttgtagcgaatttgggaaatccttcaaatctgggtgttc-cgatcaattatcccatatattccttgcatag--
| ||||| ||  | ||||||||||| ||  |||||||||||| | |||||| ||| || |  ||||||||||| |||||||| || || || ||||||| |||  | ||| ||| | ||  |||  |    ||  |     |||   | |  ||   | | | | | | | | |    |      |||||  | | || ||   
ATCTTACTGAACGCATGCAAAAGTTACTTCTTGTTATGCAAATACTAGATGGAAAAATTGCTCCAATGCTAGAGGCAGATGGGGAGCTCTTTAATAAAAAgtaagttcaaagaacaggtctattgat----ttacaaattctttatcatactctgttattattgatttccgccacaggtctgtatatatacacatagcttattc

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|32834655|gb|CD974333.1|CD974333
EST:     GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAG                         ATGGGGTTGGTTGTCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAG
genomic: GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
EST: gi|78025583|gb|DV493970.1|DV493970
EST:     GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAG                         ATGGGGTTGGTTGTCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAG
genomic: GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
EST: gi|5713778|gb|AI943770.1|AI943770
EST:     CTAGAAGCAGATGGAG-ACTTTTCAAT-AAAG                         ATGGGGTTGGTTGTCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAG
genomic: CTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
EST: gi|211089552|gb|FL477198.1|FL477198
EST:     TGGAGGAACTTTTTCAATAAAAG                         ATGGGGGTTGGTTGTCCACGTGCTGGTCTATGGGATAAGAGTCATCTTACC
genomic: TGGA-GAAC-TTTTCAATAAAAGgtacatcaat ... tcctcttaagAT-GGGGTTGGTTGT-CACGTGCTGGTCTATGGGATAAGAGTCATCTTACC
EST: gi|211089553|gb|FL477199.1|FL477199
EST:     GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAG                         ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
genomic: GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
EST: gi|148967092|gb|EE018262.2|EE018262
EST:     GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAG                         ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
genomic: GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
EST: gi|12973741|gb|BG268632.1|BG268632
EST:     GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAG                         ATGGGGTTGGTTGTCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAG
genomic: GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
EST: gi|16917596|gb|BM073359.1|BM073359
EST:     GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAG                         ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG
genomic: GAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAG

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), 45 (downstream exon)
Score: 78

AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 118

AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaat ... tcctcttaagATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTTACGGAGAGTATGCAAAAGTTGCTCATTGTTATGCAAAGATTAGATGAAAAGATCGGGCCAATGCTAGAAGCAGATGGAGAACTTTTCAATAAAAGgtacatcaatgaatatgtaaattcttattcttgtagcgaatttgggaaatccttcaaatctgggtgttccgatcaattatcccatatattccttgcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA