RetrogeneDB ID: retro_cfam_2066

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:40737381..40737896(+)
• 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_2066
ATGTCCAGTAAGTGGACCAAGGCCAAAACCACCAGGAAGCAGCCACAGCGGGCACTTCCAATGTCTTCACGATGTTTGAC
CAGTCCCAGATCCAGGAGTTTAAGGAGGCCTTCAACATGATTGACCAGAACCGAGATGGCTTCATTGACAAGGAGGACTT
GCATGACATGCTGGCCTCACTGGGAAAGAACCCCACCAATGAGTACCTCGAGGGCATGATGAGTGAGGCCCCAGGGCCCA
TCAACTTCACCATGTTTCTCACCATGTTTGGGGAGAAGCTGAATGGCACAGACCCTAAAGATGTGATCCGAAATGCCTTT
GCCTGCTTCGATAAGGAGGCTTCAGGTTTTATCCATGAGGACCACCTTCGGGAGCTGCTCACCACCATGGGTGACCACTT
CACGGACGAGGAAGTGGACGAGATGTACCGAGAGGCACCCATTGATAAGAAAGGCAACTTCAACTACGTGGAGTTCACTT
GCATTCTCAAGCATGGTGCCAAGGACAAGGACGAC

Alignment

ORF - retro_cfam_2066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSKRAKAKTTKKRPQRA-TSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEY
          MSSK..KAKTT.K.PQRA.TSNVF.MFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPT.EY
Retrocopy MSSKWTKAKTTRKQPQRA<TSNVFTMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTNEY

Parental  LEGMMSEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEV
          LEGMMSEAPGPINFTMFLTMFGEKLNGTDP.DVIRNAFACFD.EASGFIHEDHLRELLTTMGD.FTDEEV
Retrocopy LEGMMSEAPGPINFTMFLTMFGEKLNGTDPKDVIRNAFACFDKEASGFIHEDHLRELLTTMGDHFTDEEV

Parental  DEMYREAPIDKKGNFNYVEFTRILKHGAKDKDD
          DEMYREAPIDKKGNFNYVEFT.ILKHGAKDKDD
Retrocopy DEMYREAPIDKKGNFNYVEFTCILKHGAKDKDD

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	0.00 RPM	10.67 RPM
SRP017611_brain	0.00 RPM	17.39 RPM
SRP017611_kidney	0.13 RPM	201.81 RPM
SRP017611_liver	0.00 RPM	16.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2066 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2066 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,