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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcttcaagttcttgttcaagatcaagtcatccttttgtagaacactatcattcattgtgctaccttgttcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG

Basic information

species Zea mays
transcript GRMZM2G032049_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 16
gtttggcttcaagttcttgttc-aagatcaagtcatccttttgtagaacactat-cattcattg-tgctaccttgttcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG
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gtttggtcttcagtccctgctccaaaaccacatcaactcagtaaagttcttaacatgctcatggatcctccctttgttaaatttagGTTGTAATAACTAACTTGGAGGATGAAAAAGTCATAGACCTTGATGGAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAG
















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|32934107|gb|CF038919.1|CF038919
EST:     AGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAG                         GTGGTAATAACTAACTTGG
genomic: AGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAGgtttggcttc ... tcaactttagGTGGTAATAACTAACTTGG
EST: gi|32933499|gb|CF038311.1|CF038311
EST:     AGCTTAACAAAACAGCCCCTCGA-CCATGGTTGTTTTGCGACCTCTAAAG                         GTGGTAATAACTAACT
genomic: AGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAGgtttggcttc ... tcaactttagGTGGTAATAACTAACT
EST: gi|211147648|gb|FL303726.1|FL303726
EST:     AGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAG                         GTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAA
genomic: AGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAGgtttggcttc ... tcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAA

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: 49 (upstream exon), 48 (downstream exon)
Score: 260

TGACAATAGCTTAATTCGTGTTGATCGTCTAGAATATCACATCAGGGAGGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAGgtttggcttc ... tcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

TGACAATAGCTTAATTCGTGTTGATCGTCTAGAATATCACATCAGGGAGGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAGgtttggcttc ... tcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

TGACAATAGCTTAATTCGTGTTGATCGTCTAGAATATCACATCAGGGAGGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAGgtttggcttc ... tcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

TGACAATAGCTTAATTCGTGTTGATCGTCTAGAATATCACATCAGGGAGGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAGgtttggcttc ... tcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtcatccttttgtagaacactatcattcattgtgctaccttgttcaactttagGTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG
                                       ccttgttc  CT-rich tract
         ttttgta  TA-rich tract