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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcggcgtttgtggttgatcaattcaacgaacgaagcaacgggatcctgatcctgctgtgctgctgctacag

Basic information

species Zea mays
transcript GRMZM2G147051_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147051_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 5'ss of exon 5
CATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcggcgtttgtggttgatcaattcaacgaacgaa----------gcaacgggatcctgatcctgctgtgctgctgctacag-----
 |||||||| ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||| ||| || | ||||||||  |  |  | | ||  |||||  | |  ||| | |  |           ||| | | | ||   |||    | |||  | | ||      
GATGCTGAATGAGAGAAGCGATGTGTACAGCTTCGGGATCCTGATAATGGAAATCATCTCCGGTCGAAGCCCGGTCGATTACGCAAGGGCTCCAGGAGAGgttggctcttcatctg--gttgaatactgaaacaagcttatgttgtgtgtacaatgtgcttcttggccttaatttctgtgggtgcatttcag
















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|88755336|gb|DY539477.1|DY539477
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGATTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|29946455|gb|CB816158.1|CB816158
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAANCCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|71762919|gb|DR960856.1|DR960856
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGATTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|31909293|gb|CD650846.1|CD650846
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|93014131|gb|EB639651.1|EB639651
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|110532757|gb|EE036937.1|EE036937
EST:     GATCATCTCCGGCGGAAGCCCCGTTG-CTTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: GATCATCTCCGGCCGAAGCCCCGTCGAC-TACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|149061074|gb|EE157329.2|EE157329
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|71308371|gb|DR790412.1|DR790412
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|211021101|gb|FL442869.1|FL442869
EST:     GAAGCCCCGTCGATTA-GCCAAGGCCTGCCGGAGAG                         GTAAACCTGGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: GAAGCCCCGTCGACTACGCC-AGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|31909329|gb|CD650864.1|CD650864
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|30088116|gb|CB886321.1|CB886321
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|28909856|gb|CB331133.1|CB331133
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGA
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGA
EST: gi|60359282|gb|DN226255.1|DN226255
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|71315684|gb|DR794463.1|DR794463
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|31909517|gb|CD650958.1|CD650958
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|50337020|gb|CO532146.1|CO532146
EST:     ACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: ACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|93280862|gb|EB673126.1|EB673126
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|31909295|gb|CD650847.1|CD650847
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTC
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTC
EST: gi|91878715|gb|EB408672.1|EB408672
EST:     GATCATCTCCGGCCGAAGCCCCGTGGACTACGCCAGGGCCTGCCGGAGAGG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGA
genomic: GATCATCTCCGGCCGAAGCCCCGTCGACTACGCCA-GGCCTGCCGGAGA-Ggtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGA
EST: gi|28987043|gb|CB351436.1|CB351436
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|71315686|gb|DR794464.1|DR794464
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|37396493|gb|CF635537.1|CF635537
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|29167724|gb|CB410984.1|CB410984
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGA
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGA
EST: gi|31909042|gb|CD650722.1|CD650722
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|4646607|gb|AI491416.2|AI491416
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|211492061|gb|FL444499.1|FL444499
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCTTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|29129799|gb|CB380503.1|CB380503
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|71439998|gb|DR821048.1|DR821048
EST:     AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: AGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
EST: gi|71308861|gb|DR790680.1|DR790680
EST:     CCCGTCGACTACGCCAGGCCTGCCGGAGAG                         GTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG
genomic: CCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 165

CATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAGGCCATCGTGGACCCGAAGCTGCCGGAGAAGCCGTCCTCCAAGGCTCTCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 55

CATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAGGCCATCGTGGACCCGAAGCTGCCGGAGAAGCCGTCCTCCAAGGCTCTCA


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 27

CATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAGGCCATCGTGGACCCGAAGCTGCCGGAGAAGCCGTCCTCCAAGGCTCTCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 56

CATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcgg ... gctgctacagGTAAACCTTGTAGAGTGGCTCAAGAACAAGGTGACCAACAGGGACTACGAGGCCATCGTGGACCCGAAGCTGCCGGAGAAGCCGTCCTCCAAGGCTCTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGCCCCGTCGACTACGCCAGGCCTGCCGGAGAGgtcagtgcggcgtttgtggttgatcaattcaacgaacgaagcaacgggatcctgatcctgctgtgctgctgctacag

- - - - - - - - - - - - - - - - - - - - - - - - - AGATCA