RetrogeneDB ID: retro_cfam_983

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:22889540..22890284(-)
• Located in intron of: ENSCAFG00000006573

Retrocopy information

• Ensembl ID: ENSCAFG00000006577
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSCAFG00000017311
• Aliases: None
• Description: Canis lupus familiaris tropomyosin 3 (TPM3), mRNA. [Source:RefSeq mRNA;Acc:NM_001252211]

Sequence

>retro_cfam_983
ATGGCCGGGATCACCACCATCGAGGCGGTGAAGCGTAAGATCCAGGTTCTGCAGCAGCAAGCCGATGACGCAGAGGAGAG
GGCCGAGCGCCTGCAGCGGGAAGTGGAAGGGGAAAGGCGGGCCCGGGAGCAGGCTGAGGCTGAGGTGGCCTCCTTGAACC
GTAGGATCCAGCTGGTTGAAGAGGAGCTGGACCGCGCCCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAGGAAGCG
GAGAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAGAATCGAGCCTTAAAAGATGAAGAAAAGATGGAACT
CCAGGAAATCCAACTCAAAGAGGCCAAGCACATTGCAGAAGAGGCAGACCGGAAGTATGAAGAGGTGGCTAGGAAGTTGG
TGATCATTGAGGGGGACTTGGAACGTACAGAGGAACGAGCTGAGCTGGCAGAGTCCCGTTGCCGAGAGATGGATGAGCAG
ATCAGGCTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAGGAAAAGTACTCTCAAAAGGAAGACAAATATGAGGA
AGAGATAAAGATTCTCACGGATAAACTCAAGGAGGCAGAGACCCGTGCTGAGTTTGCTGAGAGATCGGTAGCCAAGCTGG
AGAAGACAATTGATGATTTGGAAGATAAGCTGAAATGCACCAAAGAGGAGCACCTGTGTACACAAAGGATGCTGGACCAG
ACTCTTCTTGACCTGAATGAGATG

Alignment

ORF - retro_cfam_983 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
Retrocopy MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL

Parental  ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
          ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
Retrocopy ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL

Parental  ERTEERAELAESKCSELEEELKNVTNNLKSLEAQAEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
          ERTEERAELAES.C.E..E.......NLK.L.A..EKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
Retrocopy ERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV

Parental  AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
Retrocopy AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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	15.92 RPM	71.19 RPM
SRP017611_brain	1.75 RPM	56.13 RPM
SRP017611_kidney	13.47 RPM	12.41 RPM
SRP017611_liver	7.69 RPM	9.21 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_983 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_983 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000015796	1 retrocopy	retro_cfam_2107,
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983 ,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,