RetrogeneDB ID: retro_cfam_2167

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:59085531..59086342(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000017231
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM1
• Ensembl ID: ENSCAFG00000016966
• Aliases: None
• Description: tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]

Sequence

>retro_cfam_2167
GACAAGAAGAATGCCTTGGATCGAGCCGAGCAGGCGGAGGCCGATAAGAGGGCTGCGGAGGACAGGAGCAAGAGCTGGAA
GATGAGCTGGTGTCGCTGCAAAAGAAACTCAAGGGCACCGAAGATGAACTGGACAAATACTCCGAGGCTGTAAAGATGCC
CAGGAGAAGTTGGAGCTGGCGGAGAAAAAGGCCACTGACGCTGAAGCCGATGTACCTTCTCTGAACAGACGCATCCAGCT
GGTTGAGGAAGAGTTGGATCGTGCCCAGGAGCGACTGACAACAGCTTTGCAGAAGCTGGAGGAGGCTGAGAAGGCAGTGG
ACGAGAGCAAGAGAGGCATGAAAGTCATTGAAAGCCGAGCCCAAAAGGATGAGGAGAAAATGGAAATTCAGGAGATTCAA
CTGAAAGAGGCCAAGCACATTGCTGAAGATGCCAACCGCAAGTATGAAGAGGTGGCCCATAAGCTGGTCATCATTGAGAG
CGACCTGGAACGCGTGGAAGAACGGGCTGAGCTCTCAGAAAGCCAAGTTCGACAGCTGGAAGAACAATTAAGAATAATGG
ATCAGACCTTGAAAGCATTAATGGCTGCAGAGGATAAGTACTCGCAGAAGGAAGACAAATATGAGGAAGAGATCAAGGTT
CTCTCTGACAAGCTGAAGGAGGCCGAGACTCGGGCTGAGTTTGCGGAGAGGTCAATAACTAAATCGGAGAAAAGCATTGA
TGACTTAGAAAAGAAAGTGGCTCATGCCAAAGAAGAAAACCTTAGTATGCATCAGATGCTGGATCAGACTTTACTGGAGT
TAAACAACATG

Alignment

ORF - retro_cfam_2167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.05 %
• Parental protein coverage: 83.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERDRVLEELHSAEDSLLAADETAA-KLEDELVSLQKKLKGTEDELDKYSEALK-DAQEKLELAEKKATDA
          .....L.....AE....AA.......LEDELVSLQKKLKGTEDELDKYSEA.K.DAQEKLELAEKKATDA
Retrocopy DKKNALDRAEQAEADKRAAEDRSK<ELEDELVSLQKKLKGTEDELDKYSEAVK<DAQEKLELAEKKATDA

Parental  EADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEA
          EADV.SLNRRIQLVEEELDRAQERL.TALQKLEEAEKA.DES.RGMKVIESRAQKDEEKMEIQEIQLKEA
Retrocopy EADVPSLNRRIQLVEEELDRAQERLTTALQKLEEAEKAVDESKRGMKVIESRAQKDEEKMEIQEIQLKEA

Parental  KHIAEDADRKYEEVARKLVIIESDLERAEERAELSESKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKY
          KHIAEDA.RKYEEVA.KLVIIESDLER.EERAELSES....LEE.L......LK.L.A...KYSQKEDKY
Retrocopy KHIAEDANRKYEEVAHKLVIIESDLERVEERAELSESQVRQLEEQLRIMDQTLKALMAAEDKYSQKEDKY

Parental  EEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEEKVAHAKEENLSMHQMLDQTLLELNNM
          EEEIKVLSDKLKEAETRAEFAERS.TK.EKSIDDLE.KVAHAKEENLSMHQMLDQTLLELNNM
Retrocopy EEEIKVLSDKLKEAETRAEFAERSITKSEKSIDDLEKKVAHAKEENLSMHQMLDQTLLELNNM

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	0.63 RPM	120.58 RPM
SRP017611_brain	0.79 RPM	103.37 RPM
SRP017611_kidney	14.59 RPM	141.85 RPM
SRP017611_liver	6.60 RPM	73.67 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2167 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2167 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Choloepus hoffmanni	ENSCHOG00000012788	11 retrocopies	retro_chof_1194, retro_chof_1272, retro_chof_1360, retro_chof_1789, retro_chof_1829, retro_chof_2309, retro_chof_346, retro_chof_399, retro_chof_412, retro_chof_770, retro_chof_967,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424,