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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcaagcctgttgattagtatcattcgattaagagtggagagacggagcaaagaaatactgttcacactcacacatacaataattgctttgaatttaacatcgatctttattatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAGCTCAAAATGGCGACCTTCCTCTTCTACGCAAACAAAACTATCATCAAAG

Basic information

species Zea mays
transcript GRMZM2G124744_T02
intron # 1
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|74237152|gb|DT645066.1|DT645066
EST:     GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAAT                         GATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
genomic: GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
EST: gi|30306389|gb|CD001062.1|CD001062
EST:     GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAAT                         GATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
genomic: GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
EST: gi|60337724|gb|DN204697.1|DN204697
EST:     ATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAAT                         GATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
genomic: ATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
EST: gi|71435545|gb|DR816595.1|DR816595
EST:     GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAAT                         GATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
genomic: GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
EST: gi|31664536|gb|CD573469.1|CD573469
EST:     GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAAT                         GATAACAAGATGGCAAAAACATTCGAC
genomic: GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGAC
EST: gi|30307020|gb|CD001693.1|CD001693
EST:     GATGATGACCCTG-GGACGGCGAAAACCCTAGATCTTTTACCGCATCAAT                         GATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG
genomic: GATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAG

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: 49 (upstream exon), 38 (downstream exon)
Score: 41

TGCCTTTCTGCAGATTTCTGATCCCAAGCTTGTTGGCTAACATGGCGAATGATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAGCTCAAAATGGCGACCTTCCTCTTCTACGCAAACAAAACTATCATCAAAG


Block sizes: 18 (upstream exon), 37 (downstream exon)
Score: 2

TGCCTTTCTGCAGATTTCTGATCCCAAGCTTGTTGGCTAACATGGCGAATGATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAGCTCAAAATGGCGACCTTCCTCTTCTACGCAAACAAAACTATCATCAAAG


Block sizes: 29 (upstream exon), 27 (downstream exon)
Score: 3

TGCCTTTCTGCAGATTTCTGATCCCAAGCTTGTTGGCTAACATGGCGAATGATGATGACCCTGTGGACGGCGAAAACCCTAGATCTTTTACCGCATCAATgtacgcaagc ... ttatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAGCTCAAAATGGCGACCTTCCTCTTCTACGCAAACAAAACTATCATCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactcacacatacaataattgctttgaatttaacatcgatctttattatttgtagGATAACAAGATGGCAAAAACATTCGACGTGGTTTCAGCGCACGGCCATCAGCTCAAAATGGCGACCTTCCTCTTCTACGCAAACAAAACTATCATCAAAG
                                       tctttatt  CT-rich tract
                                      atctttattatttgta  TA-rich tract