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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgattaacattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttgtgggccatcatattttttatggaaac...

Basic information

species Zea mays
transcript GRMZM5G868757_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 5
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgatta---acattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttgtgggccatcatattttttatggaaac-
 |||||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||| ||||||| ||||||||||||||||||||||||||||  |||    || |||| | |  || |||||||| ||  |||   |       |   ||||  ||||     |        || ||     ||| |   
CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCGgtaactgcatttcctactttctatcttccataagatattatttgcattttcatggaaattcattgt--tgttatgcataaattg--attttaagcttgggagtt

upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 5
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgatta---acattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttg--tgggccat-catattttttatggaaac
 ||| | || ||||| |||||||| |||||||||||||| || ||||| ||||||||||| |||||||| ||||||| |||||||||||||||||||||||||| |  |||    ||||||  | |  || |||||||| ||  ||  |   || | |    ||      ||  | |  | | | || |||   |   ||      
CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCGgtaattgcatttcttacattcgatctttcataagatattatttgcaatatgccaatatcatgttaattcattgttgggatagacaatgcatgaatgccat------
















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|194716906|gb|FK934065.1|FK934065
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTAC
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTAC
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     CTAAGCTTTCAATCAGTGACGTGAAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|28987392|gb|CB351612.1|CB351612
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|4609963|gb|AI600802.1|AI600802
EST:     AAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: AAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|4804325|gb|AI666191.1|AI666191
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|6020410|gb|AW065338.1|AW065338
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|60336794|gb|DN203767.1|DN203767
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211013700|gb|FL252294.1|FL252294
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgattaacattctttttagcacaagatattgttgtcatgaactcacttttcacttgtgctgttccttgtgggccatcatattttttatggaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA