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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcacattaatttacttgatacaaagcctttagttgtcttgaaagattatttcgtttgatgctaaataccttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCAGATCCAAATCTAAC

Basic information

species Zea mays
transcript GRMZM2G025854_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 11
gtagcacattaatttacttgatacaaagc-ctttagttgtcttgaaagattatttcgtttgatgctaaata----ccttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCAGATCCAAATCTAAC
|| |   || |||| |||||| |  || |  |||  || ||||||   |||   |  ||||||||| ||||    ||| |||| |||||||  ||||||||||| || || |||||||||||||| ||||| || || ||||| ||| ||||
gtggtgtatcaatt-acttgagatgaatcattttttttttcttgaggaattccattatttgatgctgaatatacacctggtttgcagGACTATATATTAAATGGTGTTCCACTTGAAGATTTTGGCAATGGTCACCCTGATCCTAATTTAAC

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 11
------------------gtagcacattaat--ttacttgatacaaagcctttagttgtcttgaaagattatttcgtttgatgctaaataccttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCAGATCCAAATCTAAC
                  || |      ||    ||||| |   |  |  |  |  | | |   ||| |  |    || |||| ||| ||  |  | |  |||| |  || | ||||||  | ||| | |||||||||||| |||||||||| ||||| ||||||||
aatgagataccttgattagttgatttccaacagctactttagggactggatacaaatctgtaagaagttactgatattggatgttaattatgtaatat--agGATTCAATTTCAAATGGAATCCCTTTGGAAGATTTTGGACATGGCCATCCTGATCCTAATCTAAC

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 11
---gtagcac-attaatttacttgatacaaagcctttag---------------ttgtcttgaaagatt-atttcgtttgatgctaaataccttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCAGATCCAAATCTAAC
    |  |   ||||||| | ||   |||    ||||||               |||| |  |   | | || | ||| |||| ||| ||  |  | |  |||| |  || | ||||||  | ||| | |||||||||||| |||||||||| ||||| ||||||||
gggatgccttgattaattgatttccaacagctactttagggactggatacaaatttgtgtgaagttactgatattgttggatgttaattatgtaatat--agGATTCAATTTCAAATGGAATCCCTTTGGAAGATTTTGGACATGGCCATCCTGATCCTAATCTAAC

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|32841182|gb|CD980863.1|CD980863
EST:     CTGGTGCTTATGCAGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCG                         GACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGTCATCCA
genomic: CTGGTGCGTATGCCGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCGgtagcacatt ... ttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCA
EST: gi|9028761|gb|BE238801.1|BE238801
EST:     CTGGTGCTTATGCAGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCG                         GACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGTCATCCA
genomic: CTGGTGCGTATGCCGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCGgtagcacatt ... ttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCA
EST: gi|32840471|gb|CD980152.1|CD980152
EST:     GGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCG                         GACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGTCATCCA
genomic: GGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCGgtagcacatt ... ttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCA
EST: gi|32839734|gb|CD979415.1|CD979415
EST:     CTGGTGCTTATGCAGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCG                         GACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGTCATCCA
genomic: CTGGTGCGTATGCCGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCGgtagcacatt ... ttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCA
EST: gi|32801890|gb|CD954126.1|CD954126
EST:     CTGGTGCTTATGCAGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCG                         GACTGCATATTA
genomic: CTGGTGCGTATGCCGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCGgtagcacatt ... ttgttttcagGACTGCATATTA
EST: gi|32943498|gb|CF048317.1|CF048317
EST:     CTGGTGCTTATGCAGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCG                         GACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGTCATCCA
genomic: CTGGTGCGTATGCCGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCGgtagcacatt ... ttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctttagttgtcttgaaagattatttcgtttgatgctaaataccttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCAGATCCAAATCTAAC
                                  tgctaaa  putative branch site (score: 2)
                                           ccttgttttc  putative PPT
             ttgaaagattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcacattaatttacttgatacaaagcctttagttgtcttgaaagattatttcgtttgatgctaaataccttgttttcagGACTGCATATTAAATGGGGTGCCTCTTGAAGATTTTGGAAATGGCCATCCAGATCCAAATCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA