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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctctcaccagcaccagtattttcaaattggacttcattttaacagcattggtaaagaacatcctttctgtttcatgcaacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG

Basic information

species Zea mays
transcript GRMZM2G081188_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 5
gtttgctctcaccagcaccagtatttt---caaattggacttca---------------ttttaacagcattggtaaagaacatcctttctgtttcatgcaacatgc-agAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG
|| ||  |||||||||    | |       || ||||||||| |               ||  || || |||| | |||| | | |||||| | |   ||||  | | |||| ||||| |||||||||||||| |||||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||
gtctgtcctcaccagctgttgcaaaccacacatattggacttaaaatatatctatctgtttcaaaaagtattgatgaagagcgttctttctttct---gcaatgttctagAATGTCGCGGCTGTTACATCAACATCAACTCGAACTCCAATTTATAAGGCCTATGCAAGAGGAGAAAACATTGGAGATGTCACTGCTAAAGGCGAATCTG

upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------gtttgctctcaccagcaccagtattttcaaattggacttcattttaacagcattggtaaagaacatcctttctgtttcatg-caacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG
                                                         | |      |     |    ||| |  | ||     |  || |  | | ||       ||  || ||||  |  |||||  |  |   ||||| || ||||| || |||||||| ||||||||||| ||||| ||||| |||| ||||| ||||||||| || || ||||||||||||||||| |||| ||
gttttactcattacttctttctttctgctcactcattcacttatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatcaactcagcagtgcagccttatttcttcatttctgctctcagAATGTTGCTGCCGTAACATCAACCTCAACTCGCACACCAATTTATAAAGCCTTTGCTAAAGGAGAAAACATAGGGGATGTCACTGCTAAAGGAGAATGTG

upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G00580.1 (Glycine max), 3'ss of exon 2
---------gtttgctctcaccagcaccagtattttcaaattggacttcattttaacagcattggtaaagaacatcctttctgtttcatg-caacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG
         ||||| |  |  |         | |  | || ||    | |  |   |||     |         |  ||| | ||||||  |  |   ||||| || |||||||| |||||||| ||||||||||| ||||| ||||| |||| ||||| |||||||||||| || ||||||||||||||||| |||| ||
gttaggtttgtttgttgacttctttctgccgactcaccaactgctaatgaactctgcagtgcaagctttttttttaatttttttttcatttctgctctcagAATGTTGCTGCTGTAACATCAACATCAACTCGCACACCAATTTATAAAGCCTTTGCTAAAGGAGAAAATATAGGGGATGTCACTGCTAAAGGAGAATGTG

upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgctctcaccagcaccagtattttcaaattggacttc-attttaacagcattggtaaa----gaacatcctttctgtttca------tgcaacat-gcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG
   |  | | | || |     |   |   |||||   ||| |||| ||    |||| |       ||   |  ||| ||| |||      ||    ||  ||||| || || || || |||||||| || ||||| || || |||||||| |||| ||||| ||||||||| || ||||| || ||||||||||| || | ||
--gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG

upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 5
gtttgctctcaccagcaccagtattttcaaattggacttcattttaacagcattggtaaagaacatcctt-tctgtttcatgcaacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG
      | | |       |   || | | |  |  |  |  |      | || || |     | ||   | | ||||| ||      || |||| || ||||| || || ||||| ||||| ||||| ||||| || || |||| ||||| ||||||||| ||||||||||||||||||||||| |||| ||
-----gtttgatggttttcttaatatgccaggtatatgttgtcaagttaccactgctgcttcatatttgtatttgtttaat------tgtagAATGTTGCTGCGGTAACGTCAACATCAACCCGCACACCAATTTACAAAGCCTTTGCTAAAGGAGAAAACATTGGAGATGTCACTGCTAAAGGAGAATGTG

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|32837137|gb|CD976815.1|CD976815
EST:     CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAG                         AATGTCGCTGCTGTTACGTCAACTTCAACTCGCACTCCAATCTATAAGGCC
genomic: CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAGgtttgctctc ... caacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCC
EST: gi|211302733|gb|FL372536.1|FL372536
EST:     CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAG                         AACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCC
genomic: CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAGgtttgctctc ... caacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCC
EST: gi|211421799|gb|FL427212.1|FL427212
EST:     CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAG                         AACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCC
genomic: CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAGgtttgctctc ... caacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCC
EST: gi|32853437|gb|CD993118.1|CD993118
EST:     CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAG                         AATGTCGCTGCTGTTACGTCAACTTCAACTCGCA
genomic: CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAGgtttgctctc ... caacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCA
EST: gi|31353527|gb|CD437884.1|CD437884
EST:     CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAG                         AATGTCGCTGCTGTTACGTCAACTTCAACTCGCACTCCAATCTATAAGGCC
genomic: CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAGgtttgctctc ... caacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCC
EST: gi|148958478|gb|EC904716.2|EC904716
EST:     ATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCCATGTTGTAAAAG                         A-CGTCGCTGCTGTTACA
genomic: ATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAA-Ggtttgctctc ... caacatgcagAACGTCGCTGCTGTTACA
EST: gi|148966241|gb|EE017202.2|EE017202
EST:     CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAG                         AACGTCGCTGCTGGTACATCAACTTC
genomic: CATTCCCTCAGTTTTTCTTGCCTATGGCTTGCGTAGCCAATGTTGTAAAGgtttgctctc ... caacatgcagAACGTCGCTGCTGTTACATCAACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcattttaacagcattggtaaagaacatcctttctgtttcatgcaacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG
     ttttaac  putative branch site (score: 2)
     ttttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctctcaccagcaccagtattttcaaattggacttcattttaacagcattggtaaagaacatcctttctgtttcatgcaacatgcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG