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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggttcttgcttgcgttgcatgcgtgggcattacaagagactctgcacgcacctagcacttgcaatttacacacgcttgctttcgtcttggacacatgttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGGCGGCGATGGAGCCCGTGTCGGCTCCAGACGACATTGCTCTAATATGCTT

Basic information

species Zea mays
transcript GRMZM2G066426_T02
intron # 2
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|211519808|gb|FL338567.1|FL338567
EST:     CTCCTCCTGGGCGATCCTTGCNAGGAC-GGCCGCGCTGCTGCAGGTTGTG                         CTNGTACC-ATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCG
genomic: CTCCTCCTGGGCGATCCTTGC-AGGACCGGCCGCGCTGCTGCAGGTTGTGgtgaggttct ... ttggtttcagCT-GTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCG
EST: gi|211192633|gb|FL310810.1|FL310810
EST:     CCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTG                         CTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGG
genomic: CCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTGgtgaggttct ... ttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGG
EST: gi|148968479|gb|EE019550.2|EE019550
EST:     CCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTG                         CTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGG
genomic: CCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTGgtgaggttct ... ttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGG

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: 44 (upstream exon), 12 (downstream exon)
Score: 4

TGGGCGCTTCGGCTGATGGAGGGCGACAGGTTCCCATCCATCGGCCTCTACCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTGgtgaggttct ... ttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGGCGGCGATGGAGCCCGTGTCGGCTCCAGACGACATTGCTCTAATATGCTT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 50

TGGGCGCTTCGGCTGATGGAGGGCGACAGGTTCCCATCCATCGGCCTCTACCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTGgtgaggttct ... ttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGGCGGCGATGGAGCCCGTGTCGGCTCCAGACGACATTGCTCTAATATGCTT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 4

TGGGCGCTTCGGCTGATGGAGGGCGACAGGTTCCCATCCATCGGCCTCTACCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTGgtgaggttct ... ttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGGCGGCGATGGAGCCCGTGTCGGCTCCAGACGACATTGCTCTAATATGCTT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 20

TGGGCGCTTCGGCTGATGGAGGGCGACAGGTTCCCATCCATCGGCCTCTACCTCCTCCTGGGCGATCCTTGCAGGACCGGCCGCGCTGCTGCAGGTTGTGgtgaggttct ... ttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGGCGGCGATGGAGCCCGTGTCGGCTCCAGACGACATTGCTCTAATATGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcacttgcaatttacacacgcttgctttcgtcttggacacatgttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGGCGGCGATGGAGCCCGTGTCGGCTCCAGACGACATTGCTCTAATATGCTT
          aatttaca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggttcttgcttgcgttgcatgcgtgggcattacaagagactctgcacgcacctagcacttgcaatttacacacgcttgctttcgtcttggacacatgttggtttcagCTGTACCCATTACCGACGTCACGGGGAGCCTCGGCGGAGCTACGGCAGCGGCGGCGATGGAGCCCGTGTCGGCTCCAGACGACATTGCTCTAATATGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA