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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataatcagattccagttggaacaactggggccaatctacacaagtgcctcctaaactctatttgtgcactagtactctttctgaggctgaagtt...

Basic information

species Zea mays
transcript GRMZM2G108416_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os03g24460.2 (Oryza sativa), 5'ss of exon 16
TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataatcagattccagttggaaca-----actggggccaatctacacaagtgcct-cctaaactctatttgtgcactagtactctttctgaggctgaagtt
|||||||| || ||||| ||||| ||||||||||||||||| || |||||||||||||||||||| |||||||| ||| ||||||| |||||||||||| |     |   | ||||||||| | || ||  | |||  | |  | |        ||     ||  |    ||      
TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggttccagttggaaaactatcagcagagccaatctaaaaaattggatacctccattggaatgacatggaagagaatttattagaact------
















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|60357806|gb|DN224779.1|DN224779
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
EST: gi|148969666|gb|EE020531.2|EE020531
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
EST: gi|6827209|gb|AW330852.1|AW330852
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
EST: gi|211381070|gb|FL456665.1|FL456665
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
EST: gi|78179722|gb|DV550095.1|DV550095
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
EST: gi|149084134|gb|EE173537.2|EE173537
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
EST: gi|60352318|gb|DN219291.1|DN219291
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
EST: gi|78115926|gb|DV534314.1|DV534314
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTTGTGGTGAAAGAAAACTTTGTGTTACATGAAC
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTT-GTGGTGAAAGAAAACTTTGTGTTACATGAAC
EST: gi|12058174|gb|BF733074.1|BF733074
EST:     TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACT                         GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT
genomic: TATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATT

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: 47 (upstream exon), 49 (downstream exon)
Score: 131

TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 155

TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 214

TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 194

TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataa ... aaaataacagGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataatcagattccagttggaacaactggggccaatctacacaagtgcctcctaaactctatttgtgcactagtactctttctgaggctgaagtt

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