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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatcactgacgatgagtgtcgacttccctttccagttcctcattttgctaacatctcgccatccgccctacctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGATCAAACTCGATGTGTGGCACTCTCGAGTACATGGCCCCGGAAATTGTTC

Basic information

species Zea mays
transcript GRMZM2G080001_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080001_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g48290.1 (Oryza sativa), 3'ss of exon 4
gtaagaatcactgacgatgagtgtcgacttccctttccagttcctcattttgctaacatctcgccatccgccctacctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGATCAAACTCGATGTGTGGCACTCTCGAGTACATGGCCCCGGAAATTGTTC
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gtaagaatgcctt-cttcaacaatctcctcctgctacttcttttccattttgctgatatcttttttgttgcctca--tttcaagGCCATGCTCACTGACTTTGGCCTTGCCAAAGAATTTAATGAGAATACAAGATCAAACTCGATGTGTGGAACAGTTGAGTATATGGCCCCAGAGATTATTC
















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|78119270|gb|DV537654.1|DV537654
EST:     CAAGCCCGAAAACATCCTTCTGGATGCTGATGGGCAT                         GCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGA
genomic: CAAGCCCGAAAACATCCTTCTGGATGCTGATGGCCATgtaagaatca ... acctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGA
EST: gi|76282647|gb|DV022215.1|DV022215
EST:     CAAGCCCGAAAACATCCTTCTGGATGCTGATGGCCAT                         GCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGA
genomic: CAAGCCCGAAAACATCCTTCTGGATGCTGATGGCCATgtaagaatca ... acctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGA

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: 47 (upstream exon), 47 (downstream exon)
Score: 73

TACAGCTGAAATTGTATCTGCTGTAGCGCATCTTCATGCTAATGGAATTATGCATAGGGATCTCAAGCCCGAAAACATCCTTCTGGATGCTGATGGCCATgtaagaatca ... acctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGATCAAACTCGATGTGTGGCACTCTCGAGTACATGGCCCCGGAAATTGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 139

TACAGCTGAAATTGTATCTGCTGTAGCGCATCTTCATGCTAATGGAATTATGCATAGGGATCTCAAGCCCGAAAACATCCTTCTGGATGCTGATGGCCATgtaagaatca ... acctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGATCAAACTCGATGTGTGGCACTCTCGAGTACATGGCCCCGGAAATTGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

TACAGCTGAAATTGTATCTGCTGTAGCGCATCTTCATGCTAATGGAATTATGCATAGGGATCTCAAGCCCGAAAACATCCTTCTGGATGCTGATGGCCATgtaagaatca ... acctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGATCAAACTCGATGTGTGGCACTCTCGAGTACATGGCCCCGGAAATTGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

TACAGCTGAAATTGTATCTGCTGTAGCGCATCTTCATGCTAATGGAATTATGCATAGGGATCTCAAGCCCGAAAACATCCTTCTGGATGCTGATGGCCATgtaagaatca ... acctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGATCAAACTCGATGTGTGGCACTCTCGAGTACATGGCCCCGGAAATTGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctttccagttcctcattttgctaacatctcgccatccgccctacctttctagGCCATGCTCACAGACTTTGGCCTTGCGAAGGAATTCTGTGAAAATACCAGATCAAACTCGATGTGTGGCACTCTCGAGTACATGGCCCCGGAAATTGTTC
                     tgctaac  putative branch site (score: 149)
                                     tccgccctacctttct  putative PPT
               tcatttt  TA-rich tract