dme-mir-997

dme-mir-997

The complete D. yakuba ortholog appears missing and could not be found from assembly nor trace data searches.

A search of the yakuba genome assembly with the D. sechellia ortholog found 15 hits, but these hits only captured the star sequence partially and did not span the mature sequence (one example is shown below).

dse-mir-997	CAATAAATATGTAGTTTTAGATACTCGCCAGTCAGGATGCTCTGTCAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAGGAGCGGCAGACCTGGAGAAGTTTTCAGAGCCAACAAAATTCATATGATGATGCATTTTCAGTCTCTGAAAATTTCTTCAGCAGAAGTTGATTTTAGCGAAGTGAAGCTCATTCGATTTTGATCATACTAACATTTGTGGATGCTTGGATCGTCAGTTTGGTGGAATATT
gnl\|ti\|386447040:428-513	CG-------------------------------------------------------------------------------------------------------------------------ACACAATTTATTTAATGATGCATTTTCAGTCCCTGAAATCTTCTTCAGTAAAAGTGGATTTTTGTAAAGTTGAGCTCATTCGA------------------------------------------------------

Searching the yakuba genome assembly with the D. erecta ortholog did not return any hits.

Changes

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droSim1	chr3R	6329178	G	3	0	0	0	0	0	0.588	0.059	0.353	0	17	Ambiguous - The two alleles agree with either melanogaster or sechellia.	Loop
droSim1	chr3R	6329213	A	3	0	0	0	0	0	0.444	0.5	0	0.056	18	Ambiguous - Suggested base change does not agree with neighboring species	Loop
droSim1	chr3R	6329258	A	3	0	0	0	0	0	0.222	0	0.778	0	18	Valid - genomic error	Loop
droSim1	chr3R	6329337	T	3	0	0	0	0	0	0	0.526	0	0.474	19	Ambiguous - Suggested base change does not agree with neighboring species	3' flanking region
droSim1	chr3R	6329349	C	3	0	0	0	0	0	0	0.421	0	0.579	19	Valid - Genomic Error	3' flanking region

Corrected alignment

dme-mir-997

Species	Coordinate	Alignment
dm3	chr3R:15152661-15152905 -	CAATTAA-TATGTAGTTTA---------------TGGAT-----CCTCTTTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAAGAGCGACAGTC-CTGGAGAAGTTATCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCC--------GTCTCTGAAAACGTCTTCAG-CAGAAGTTGTTTTTAGCGAAGTGAAACTCATT-CGATTTTGATCATACTA-ACGA---CATTGGAT------G-CTTG-----GATCGGCA----GTTTGGTGGAATATA
droSim1	chr3R:6329088-6329350 +	CAATAAA-TATGTAGTTTTGGATACTCGCCAGTCAGGAT-----GCTCTGTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCA--------GTCTCTGAAAACTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATT-CGATTTTGATCATACTA-ACGACATTTGTGGAT------G-CTTG-----GATCGGCA----GTTTGGTGGAATATT
droSec1	super_25:615309-615568 +	CAATAAA-TATGTAGTTTTAGATACTCGCCAGTCAGGAT-----GCTCTGTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAACAAAATTCATA-TGATGATGCATTTTCA--------GTCTCTGAAAATTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATT-CGATTTTGATCATACTA-A---CATTTGTGGAT------G-CTTG-----GATCGTCA----GTTTGGTGGAATATT
droYak2	chrU:8935876-8936155 -	AAAATAAAAGTTGAATTTTGAAAAATAAA--ATTTCCAA-----TTTTTGACCATGATTTTTGAACGTTTGCCGAAAATCGT----GTTTCTGCGACTATAAATATCCGTATTTTGATCATAACTTTCGAAATATTGGTCCAATCA-TGGAATGCCACAC-CTCGTTGAGTTC-----------------------GTAATTAAATTTCCAATCGAACTGTGTTTA---------AAAA-TAAAAGTTGAATTTTGAAAAATAAAATTT--CCAATTTTTGACCATG---------ATTTTTGAAC------G-TTTGCCGAAAATCG--T----GTTTCTGCGACTATA
droEre2	scaffold_4784:21223629-21223900 -	CAAGACG--------CCTTAAA-----GCGAGTTCAGCTTTACTGTTCTA-GAATGCAGTTTAT----ATACCCAAACTCGAAGGAGTTCCACA------------------------------------------------TTAAGAAGAGCAGCAGAAGCAGAAAAAAATGTCTGGACCCTTGAAATTCATTTTGCAAATGCATTTCCATT------GGCTCGGAAATCTTTCTCTGTCAGGTGTTGATTTTTTAAAAGTGGAGCTCATT-CGATTTTGAATATATAAAATAACAGTTCTTGATATGTATGAGTTG-----GATTTGCACCTTGTCTGACAGAAAAAC
droAna3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------