RetrogeneDB ID: retro_cfam_2071

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:44011776..44012189(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MYL9
• Ensembl ID: ENSCAFG00000008540
• Aliases: None
• Description: Canis lupus familiaris myosin, light chain 9, regulatory (MYL9), mRNA. [Source:RefSeq mRNA;Acc:NM_001252166]

Sequence

>retro_cfam_2071
ATGTCCAGTAAGCGGGCCAAGGCCAAAACCACCAAGAAGCGGCCACAGCGGGCCACTTCCAATGTCTTCGGATGTTTGAC
CAGTCCCAGATCCAGGAGTTTAAGGAGGCCTTCAACATGATTGACCAGAACCAAGATGGCTTCATTGACAAGGAGGACTT
GCATGACATGCTGGCCTCACTGGGAAAGAACCCCACTGATGAGTACCTCGAGGGCATGATGAGTGAGGCCCCAGGGCCCA
TCAACTTCACCATGTTTCTCACCATGTCTGGGGAGAAGCTGAATGGCACAGACCCTGAAGATGTGATCTGAAATGCCTTT
GCCTGCTTCGATGAGGAGGCCTCAGGTTTTATCCATGAGGACCACCTTCGGGAGCTGCTCACCACCATAGGTGACCGCTT
CACGGAGGAGGAA

Alignment

ORF - retro_cfam_2071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.96 %
• Parental protein coverage: 80.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSKRAKAKTTKKRPQRATSNVFA-MFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEY
          MSSKRAKAKTTKKRPQRATSNVF..MFDQSQIQEFKEAFNMIDQN.DGFIDKEDLHDMLASLGKNPTDEY
Retrocopy MSSKRAKAKTTKKRPQRATSNVFG<MFDQSQIQEFKEAFNMIDQNQDGFIDKEDLHDMLASLGKNPTDEY

Parental  LEGMMSEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEE
          LEGMMSEAPGPINFTMFLTM.GEKLNGTDPEDVI.NAFACFDEEASGFIHEDHLRELLTT.GDRFT.EE
Retrocopy LEGMMSEAPGPINFTMFLTMSGEKLNGTDPEDVI*NAFACFDEEASGFIHEDHLRELLTTIGDRFTEEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.13 RPM	10.67 RPM
SRP017611_brain	0.08 RPM	17.39 RPM
SRP017611_kidney	2.18 RPM	201.81 RPM
SRP017611_liver	0.15 RPM	16.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2071 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2071 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2071 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008540	3 retrocopies	retro_cfam_1384, retro_cfam_2066, retro_cfam_2071 ,
Canis familiaris	ENSCAFG00000029134	3 retrocopies	retro_cfam_166, retro_cfam_583, retro_cfam_79,
Canis familiaris	ENSCAFG00000032168	1 retrocopy	retro_cfam_1224,
Callithrix jacchus	ENSCJAG00000012890	4 retrocopies	retro_cjac_3193, retro_cjac_3195, retro_cjac_3743, retro_cjac_637,
Equus caballus	ENSECAG00000007545	1 retrocopy	retro_ecab_923,
Homo sapiens	ENSG00000101335	1 retrocopy	retro_hsap_956,
Gorilla gorilla	ENSGGOG00000024477	1 retrocopy	retro_ggor_770,
Myotis lucifugus	ENSMLUG00000000207	2 retrocopies	retro_mluc_2534, retro_mluc_327,
Nomascus leucogenys	ENSNLEG00000006109	1 retrocopy	retro_nleu_2460,
Pongo abelii	ENSPPYG00000010971	1 retrocopy	retro_pabe_972,
Pan troglodytes	ENSPTRG00000013458	1 retrocopy	retro_ptro_662,