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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG

Basic information

species Zea mays
transcript GRMZM2G044819_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaact---------gaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
|||||| | |||  ||||    | ||||| |  | | |||||  | | ||  |          ||||||| || |||||   |   || ||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| |||||||||
gtgagtggttatggttttgcagtggtgaatattatt-ttatgagcccaaattttatctgtgtaaatgcaatta-ttttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG

upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 16
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaact---------gaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG---------------------
|||||| | |||  ||||    | ||||| |  | | |||||  | | ||  |          ||||||| || |||||   |   || ||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| |||||||||                     
gtgagtggttatggttttgcagtggtgaatattatt-ttatgagcccaaattttatctgtgtaaatgcaatta-ttttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAGGTAATTGCAAAACTCTAGATG

upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
--------gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgc--aactaattttgcat-ttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
         | ||| | ||  | ||  | |   |||     | | |     |   |    |  || |  ||||  ||     | ||  || |||||||||||||| || ||||| ||||| ||||||||| || | ||||| || |||||||||||||  ||||| ||||||
gtatgtggtttagtggttacttattgatgaccctgatctctattttatcacattactcttttgatactgaactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG

upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 15
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggac-accaaactga-atgcaactaattttgcatt--tcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
||  ||   ||  ||||| | |   |||     | | |     |  ||     ||| ||  ||||  ||     ||  |  || |||||||||||||| || ||||| ||||| ||||||||| || | ||||| || |||||||||||||  ||||| ||||||
gtatgtgcttacttttttatgaccctgatctctattttatcacattactcttttgatattgaactgtttaaattttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG

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:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|78025583|gb|DV493970.1|DV493970
EST:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|5713778|gb|AI943770.1|AI943770
EST:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|211089552|gb|FL477198.1|FL477198
EST:     CCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: -CACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|211089553|gb|FL477199.1|FL477199
EST:     TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|148967092|gb|EE018262.2|EE018262
EST:     TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|12973741|gb|BG268632.1|BG268632
EST:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|16917596|gb|BM073359.1|BM073359
EST:     TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaatgttatggacaccaaactgaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
                                aactaat  putative branch site (score: 2)
                                           catttcct  putative PPT
                                aactaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC