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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgtgtcgtcgtctcgtccctgtcgaccctccccactgcccccgagtcccagtctcccagactgagtcgcctcacgtggcgtgccgttgggtttgtctgtcctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAGGTGGAGTACCTGGAGTCTTCGGTGCGCGTCGCCGGCAGGAAGCAGCGCG

Basic information

species Zea mays
transcript GRMZM2G030712_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030712_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g05480.1 (Oryza sativa), 3'ss of exon 7
gtacgtgtgtcgtcgtctcgtccc--tgtcgaccctccccactgcccccgagtcccagtctcccagactgagtcgcctcacgtggcgtgccgttgggtttgtctgtcctg-cctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAGGTGGAGTACCTGGAGTCTTCGGTGCGCGTCGCCGGCAGGAAGCAGCGCG
||||||      | |  ||||  |  || |    |    ||| | |      |||    |        |   | |       |   |           |||| |||   |   |||||||| | || ||||||||||||||| | ||||||||||||||||| ||||||||||||||||||||||| ||||||||||  ||  ||| |||| ||   |
gtacgtacaatcttgaatcgtttcattggcagatcgaaacacagtctt----tcctgaacaaaatattttcattgttcagaattcagattaagaattcttgtgtgtttggatttgcagCTGAGAGTTTACACGGCGGAGGACATCTCGAACGAGCTGGAGCGAGCCAAGGTGGAGTACCTGGAGTCGTCGGTGCGCGCGGCGAGCAAGAAGAAGGTGG
















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|211056577|gb|FL481911.1|FL481911
EST:     GCCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCCCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: G-CCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|149027590|gb|EE046581.2|EE046581
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|29130825|gb|CB381529.1|CB381529
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|60399493|gb|DN232305.1|DN232305
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|78113611|gb|DV532002.1|DV532002
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|28930819|gb|CB334180.1|CB334180
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|29129867|gb|CB380571.1|CB380571
EST:     CAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: CAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|30306390|gb|CD001063.1|CD001063
EST:     AACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG

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 3 RNA-Seq libraries.


Block sizes: 11 (upstream exon), 39 (downstream exon)
Score: 2

CGACGACGGACAGACGGATCTGCTGCACTCGTACGGGCTAGGGTATCCCGAGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAGGTGGAGTACCTGGAGTCTTCGGTGCGCGTCGCCGGCAGGAAGCAGCGCG


Block sizes: 17 (upstream exon), 47 (downstream exon)
Score: 3

CGACGACGGACAGACGGATCTGCTGCACTCGTACGGGCTAGGGTATCCCGAGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAGGTGGAGTACCTGGAGTCTTCGGTGCGCGTCGCCGGCAGGAAGCAGCGCG


Block sizes: 10 (upstream exon), 40 (downstream exon)
Score: 3

CGACGACGGACAGACGGATCTGCTGCACTCGTACGGGCTAGGGTATCCCGAGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAGGTGGAGTACCTGGAGTCTTCGGTGCGCGTCGCCGGCAGGAAGCAGCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagactgagtcgcctcacgtggcgtgccgttgggtttgtctgtcctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAGGTGGAGTACCTGGAGTCTTCGGTGCGCGTCGCCGGCAGGAAGCAGCGCG
            gcctcac  putative branch site (score: 3)
                                       tctgtcct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgtgtcgtcgtctcgtccctgtcgaccctccccactgcccccgagtcccagtctcccagactgagtcgcctcacgtggcgtgccgttgggtttgtctgtcctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAGGTGGAGTACCTGGAGTCTTCGGTGCGCGTCGCCGGCAGGAAGCAGCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG