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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctggatttttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG

Basic information

species Zea mays
transcript GRMZM2G006130_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 3
gtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagc---tggatttttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG
                 | |   |        |  ||  ||  |  | |||| ||| |  || |||||  |   |   |  | |    ||  |    |||   ||  ||||     ||||||| |||||||||||| ||||||| ||||||||||| || || |||||||| |||||||||||||| ||| | || |||||||||||||| || |||||
-----------------ggagcataaactggatgggatgcaaaataatatgccctt-tcatggaagcta-tattgacatgtagggcttagtataaccagcttatgagttttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGAGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG

upper sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 3
gtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctg-gatttttactt-cagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG
                | ||     |   |    || || || |    |||| ||| ||||||| | |          ||   ||| |   |     |  |  || |||||    ||||||| |||||||||||| ||||||| ||||||||||| || || |||||||| ||||| |||||||| ||| | || |||||||||||||| || |||||
--------------gattaagagcataaactcgatggaaaataat---atgccctttttttgaa-gttatattgacatttagggtttagtataaccaacttatgagttttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG
















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|8367215|gb|BE050160.1|BE050160
EST:     GGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCCGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: GGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|60399112|gb|DN231926.1|DN231926
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|32844992|gb|CD984673.1|CD984673
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|32929289|gb|CF034101.1|CF034101
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|88755664|gb|DY539805.1|DY539805
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|32844324|gb|CD984005.1|CD984005
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211170721|gb|FL129164.1|FL129164
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAATACATTGACCCGTGGTCC
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAA-ACATCGACCCGTGGTCC
EST: gi|91051534|gb|EB161952.1|EB161952
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagctgctgccggtgttgatgttcaaggttttggagctggatttttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG
               tgttgat  putative branch site (score: 4)
                                           tttttacttc  putative PPT
                                          atttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctggatttttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC