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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccgcccctctccgatccctcgatttcacttcactttgcttttgcgttggttcaccggggcctgaaccgattggttgggtttggtttcctgcgcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG

Basic information

species Zea mays
transcript GRMZM2G058366_T01
intron # 10
splice site 3'
intron type U2

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|148965008|gb|EE015841.2|EE015841
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211158731|gb|FL327701.1|FL327701
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211340444|gb|FL354255.1|FL354255
EST:     GGTCGGCAAGA-CTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAACAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211435902|gb|FL357604.1|FL357604
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|20803409|gb|BQ294459.1|BQ294459
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAACAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211522124|gb|FL314742.1|FL314742
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|15100485|gb|BI396276.1|BI396276
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAACAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|60353761|gb|DN220734.1|DN220734
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211093130|gb|FL308874.1|FL308874
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211267809|gb|FL345566.1|FL345566
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211403760|gb|FL312287.1|FL312287
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|149062811|gb|EE157528.2|EE157528
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211495186|gb|FL341359.1|FL341359
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211477104|gb|FL313896.1|FL313896
EST:     GGTCGGCAAGA-CTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
EST: gi|211165712|gb|FL359024.1|FL359024
EST:     GGTCGGCAAGACCTCGCTGATGAACCA                         GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA
genomic: GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGA

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), 48 (downstream exon)
Score: 348

GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 213

GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 136

GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GGTCGGCAAGACCTCGCTGATGAACCAgtaagtccgc ... gcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccgcccctctccgatccctcgatttcacttcactttgcttttgcgttggttcaccggggcctgaaccgattggttgggtttggtttcctgcgcgcgcgcagGTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG