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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccactgattggtagcactgcgttagagctcttcaatgattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG

Basic information

species Zea mays
transcript GRMZM5G824405_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g18310.3 (Oryza sativa), 3'ss of exon 9
gtaggccactgat--tggtagcactgcgttagagctcttcaatgattaa--ctttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
||| |  |    |  ||||   | |  ||||   | ||   || ||| |  |||    ||||||   |||| ||||| || ||||||||||||||||||||||  ||||| || ||||||||||||||||| ||||| || ||||||
gtaagttagaagttttggtgatattctgttattacgctg-gataatttattcttctttctggtccatagGTAGGTATCTTTGATGCCACAAACAGCACAAGAAACCGGAGAAATATGCTGATGAAAATGGCGGAAGGCAAGTGTAAG

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 12
gtaggccact------gattggtagcactgcgttaga--gctcttcaatgat--------taactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
|||   || |      || |  |     | | |||    | ||||  ||| |        ||| ||| |  |    |  ||||||| || || |||||||||||||| |  |    ||| || ||||||||||||||| |||||||||||| ||| |||
gtaaatcattcttgttgaatacttttgttactttaatatgttctttcatgttattttgcataagttttaatttcgatttagGTTGGGATATTTGATGCCACAAACAGTAGCAAGGAACGAAGAAACATGCTGATGAAATTGGCTGAAGGAAGATGCAAG

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaggccactgattggtagcac-tgcgttagagctcttcaatgattaactttcagctggt------ctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
||| |   ||    | |   |  |  |||   | | |  |    ||   ||  |  | ||      ||| ||||||| || || ||||| || || |||||| || | ||  |||| ||| |||||||||||||||||||||| ||||||
gtaagtatctttcggtttagatgtaagttcctggtttctatatcttgcattgtaaatagtttttagctgtagGTTGGAATCTTTGATGCAACTAATAGCACACGAGTTCGACGGAATATGTTGATGAAAATGGCTGAAGGAAAGTGTAAG

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 10
----------gtaggccactgattggtagcactgcgttagagctcttcaat---gattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
           || | ||   ||||  |    || |    | |  |||| |    ||||  ||  |  |||  || ||||||| || ||||||||||||||||| || || | ||| ||||| |||||||||||||||||||| ||||| || |||
gtaagttattttatgtcagatattgtgatgcatgtgcctaatcctttcattttaaatta--ttctaattggattgtagGTTGGAATATTCGATGCCACAAACAGTACCAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAG

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|84980594|gb|DW530943.1|DW530943
EST:     CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAG                         GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
genomic: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
EST: gi|19437252|gb|BM953662.1|BM953662
EST:     CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAG                         GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
genomic: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
EST: gi|22491067|gb|BU050990.1|BU050990
EST:     CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAG                         GTTGGTATTTTCGATGCCACAAACAGCACAAGAATGCGGAGGAACATGCTG
genomic: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggtagcactgcgttagagctcttcaatgattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
                               gattaac  putative branch site (score: 2)
                            aatgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggccactgattggtagcactgcgttagagctcttcaatgattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA