RetrogeneDB ID: retro_cfam_1640

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:4900067..4900433(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCO1
• Ensembl ID: ENSCAFG00000013472
• Aliases: None
• Description: transmembrane and coiled-coil domains 1 [Source:HGNC Symbol;Acc:18188]

Sequence

>retro_cfam_1640
AAAAAGAAAATAGAGAGGCAAGAAGAGGAACTGAAAAATAACAATGGGGACCTATCCATGGTCCGAATGAAATCCATGTT
TGCAACTGGCTTTTGTTTTACTGCCCTAATGGGAATGTTCAATTCTATATTTGATGGTAGAGTGGTGGCAAAACTCCCTT
TCACCCCTCTTTCCTATATCCAAGGACTGTCTCATTGAAACCTGCTGGGGGATGATACCACAGACTGTTCCTTCATCTTT
CTGTATATTCTCTGTACCATGTCAATTTGATAGAACATCCAGAAGATTCTTGGTCTTGCCCCTTCACATGCTGCCACCAA
GCAGGCAGGTGGATTTCTTGGCCCTCCACCTCCTTCTGGAAAGTTC

Alignment

ORF - retro_cfam_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.26 %
• Parental protein coverage: 64.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKKIERQEEKLKNNNRDLSMVRMKSMFAIGFCFTALMGMFNSIFDGRVVAKLPFTPLSYIQGLSHRNLLG
          KKKIERQEE.LKNNN.DLSMVRMKSMFA.GFCFTALMGMFNSIFDGRVVAKLPFTPLSYIQGLSH.NLLG
Retrocopy KKKIERQEEELKNNNGDLSMVRMKSMFATGFCFTALMGMFNSIFDGRVVAKLPFTPLSYIQGLSH*NLLG

Parental  DDTTDCSFIFLYILCTMSIRQNIQKILGLAPSRAATKQAGGFLGPPPPSGKF
          DDTTDCSFIFLYILCTMSI..NIQKILGLAPS.AATKQAGGFLGPPPPSGKF
Retrocopy DDTTDCSFIFLYILCTMSI**NIQKILGLAPSHAATKQAGGFLGPPPPSGKF

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	20.12 RPM
SRP017611_brain	0.00 RPM	13.89 RPM
SRP017611_kidney	0.00 RPM	59.04 RPM
SRP017611_liver	0.00 RPM	15.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1640 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1640 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010009	1 retrocopy	retro_btau_1441,
Canis familiaris	ENSCAFG00000013472	2 retrocopies	retro_cfam_1640 , retro_cfam_833,
Echinops telfairi	ENSETEG00000009382	2 retrocopies	retro_etel_1552, retro_etel_570,
Macropus eugenii	ENSMEUG00000011045	2 retrocopies	retro_meug_894, retro_meug_997,
Monodelphis domestica	ENSMODG00000001335	2 retrocopies	retro_mdom_1319, retro_mdom_334,
Oryctolagus cuniculus	ENSOCUG00000008441	2 retrocopies	retro_ocun_1148, retro_ocun_1642,
Sarcophilus harrisii	ENSSHAG00000016602	1 retrocopy	retro_shar_790,