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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT

Basic information

species Zea mays
transcript GRMZM2G141587_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
-atcatgattttttt-taaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgata-tactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
 ||  || | || |  ||||| |   ||  | |||      | || |||   || || |  |   |     |||| ||| || |  |    ||||  |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || |||||||||||||| |||||||| ||||
gattctgttgttgtagtaaaattaaattaatctcaaat---ctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
atcatgattttttt-taaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggtta--atgatat-actggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
     | ||||    |   ||||||   ||   ||  ||   |  |  | || |  || || ||||| |||   ||| ||| | |  |    ||||  ||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||| ||||| || || ||||||||||| |||||||| ||||
----cggttttgaaattgtacttgtcgggttaaataaatgtgatgaacttttctacgttctggtttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
-atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
     ||| ||||   | ||      || |  |  |   |           |||||||  ||     |||   |||| |  || | | || | |  | |||| ||||| ||||||||| |||||||| ||||| ||||||||||||||||| || ||||| |||||||| || || ||||||||||| || |||||||| |
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgggtggtggctgat-tgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
-atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
     ||| ||||   | ||      || |  |  |   |       |   |||||||   |     ||| | | || |  || | | || | |  | |||| ||||| ||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| |||||||| || || ||||||||||| || |||||||| |
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttat-tgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagttta--ggttaatgatatactggtgtgatatt-tgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
 | |     |  |  |   |||  |||   | ||    ||     ||| || ||  |||  ||| |  |||   |||  |  || | |  | || |  |  |||||||||||||||||||||||||||| ||||| ||||| ||||||||||| || || || |||||||| |  || ||||||||||| ||||||||||| |
-taaaataataatccaccccttagttttaattatcaccacttatttatttt-ttcatgcatgttgactggtgtctgacttg-tgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagttta--ggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
| | | |   |  | |        || || | |   ||  |  | | | || |||  ||  ||| |  |||   |||  |  || | |  | ||  | ||||||| ||||||||||||| |||||||| || || ||||| ||||||||||| ||||| || |||||||| || || ||||||||||| ||||||||||| |
agctttaaaataataatctgccccttagttttaattatttccactt-ttttttttaagcatgttgactggtgtctgacttg-tgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatc-ttatttgtgctagt-ttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
    | |  |    | ||   |  |||    |||  ||   |   |||  |||||| || |    ||   ||  |  | |  |  | |  | | ||||||||||  |||  || || || |||||||| ||||| ||||| ||||||||||| || ||||| ||||| ||||| || |||||||| || || || ||||| |
gcattaagctaggatgaatgattgtttccaccat--attttaatttattgttatttatgtttacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgt-gctagttta-ggttaatga--tatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
       |||| | ||| |     |   |   ||   | |  ||  |  || ||||| |  |  ||| |||||||||  | |  |  | || | ||  ||||||||||| | ||||||| | ||||| || | ||| ||||| ||||| ||||| |||||||||||||||||| | || ||||||||||| ||||||||||| |
----actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT

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|60341035|gb|DN208008.1|DN208008
EST:     GGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA                         AGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGA
genomic: GGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAAgtaagtttac ... tttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGA
EST: gi|32928123|gb|CF032935.1|CF032935
EST:     GGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA                         AGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGA
genomic: GGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAAgtaagtttac ... tttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttatttgtgctagtttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
                     ggttaat  putative branch site (score: 4)
                                             tttgtttc  putative PPT
                       ttaatgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA