RetrogeneDB ID: retro_cfam_876

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:31320310..31321021(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004917
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMBIM6
• Ensembl ID: ENSCAFG00000008400
• Aliases: None
• Description: Canis lupus familiaris transmembrane BAX inhibitor motif containing 6 (TMBIM6), mRNA. [Source:RefSeq mRNA;Acc:NM_001252399]

Sequence

>retro_cfam_876
ATGAACATATTTGATCGGAAGATCAACTTTGATGCACTCTTAAAATTTTCCCACATAACCCCCTCTACACAGCAGCACCT
GAAGAAGGTCTATGCCAGTTTTGCTCTCTGTATGTTCGTGGCAGCTGCAGGGGCCTATGTCCATGTGGTCACTCATTTCC
TTCAGGCTGGCCTGCTCTCTGCCTTGGGCTCCCTGGGGTTGATGATTTGGCTGATGGCAACACCTCATAGCCATGAAACT
GAGCAAAAAAGACTGGGACTTCTTGCTGGATTTGCTTTCCTTACAGGAGTTGGCCTGGGCCCTGCTCTGGAGCTGTGCAT
TGCCATCAACCCCAGCATTCTTCCCACTGCCTTCATGGGCACAGCAATGATCTTTACCTGCTTCACCCTGAGTGCCCTCT
ATGCCAGGCGCCGGAGCTACCTCTTTCTGGGAGGTGTCTTGATGTCAGCCATGAGTCTGATGCTCTTATCTTCCCTGGGG
AACCTTTTCTTTGGATCCATTTGGCTTTTCCAGGCAAACCTGTATGTGGGGCTGGTGGTCATGTGTGGCTTTGTCCTTTT
TGATACTCAACTCATTATTGAAAAGGCTGAAAATGGAGATAAGGATTATATCTGGCACTGCGTTGACCTCTTCTTAGATT
TCGTTACCCTCTTCAGAAAACTCATGATGATCCTGGCTATGAATGAGAAGGACAAGAAGAAAGAGAAGAAG

Alignment

ORF - retro_cfam_876 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MNIFDRKINFDALLKFSHITPSTQQHLKKVYASFALCMFVAAAGAYVHVVTHFLQAGLLSALGSLGLMIW
          MNIFDRKINFDALLKFSHITPSTQQHLKKVYASFALCMFVAAAGAYVHVVTHFLQAGLLSALGSLGLMIW
Retrocopy MNIFDRKINFDALLKFSHITPSTQQHLKKVYASFALCMFVAAAGAYVHVVTHFLQAGLLSALGSLGLMIW

Parental  LMATPHSHETEQKRLGLLAGFAFLTGVGLGPALELCIAINPSILPTAFMGTAMIFTCFTLSALYARRRSY
          LMATPHSHETEQKRLGLLAGFAFLTGVGLGPALELCIAINPSILPTAFMGTAMIFTCFTLSALYARRRSY
Retrocopy LMATPHSHETEQKRLGLLAGFAFLTGVGLGPALELCIAINPSILPTAFMGTAMIFTCFTLSALYARRRSY

Parental  LFLGGVLMSAMSLMLLSSLGNLFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDKDYIWHCVDL
          LFLGGVLMSAMSLMLLSSLGNLFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDKDYIWHCVDL
Retrocopy LFLGGVLMSAMSLMLLSSLGNLFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDKDYIWHCVDL

Parental  FLDFVTLFRKLMMILAMNEKDKKKEKK
          FLDFVTLFRKLMMILAMNEKDKKKEKK
Retrocopy FLDFVTLFRKLMMILAMNEKDKKKEKK

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	0.29 RPM	264.55 RPM
SRP017611_brain	0.40 RPM	250.01 RPM
SRP017611_kidney	2.91 RPM	1552.60 RPM
SRP017611_liver	1.67 RPM	706.64 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_876 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_876 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
Bos taurus	ENSBTAG00000018588	1 retrocopy	retro_btau_762,
Canis familiaris	ENSCAFG00000008400	2 retrocopies	retro_cfam_1220, retro_cfam_876 ,
Callithrix jacchus	ENSCJAG00000021032	1 retrocopy	retro_cjac_272,
Dasypus novemcinctus	ENSDNOG00000007882	2 retrocopies	retro_dnov_164, retro_dnov_857,
Macropus eugenii	ENSMEUG00000015590	4 retrocopies	retro_meug_1076, retro_meug_1706, retro_meug_2157, retro_meug_48,
Monodelphis domestica	ENSMODG00000004277	2 retrocopies	retro_mdom_210, retro_mdom_250,
Otolemur garnettii	ENSOGAG00000005137	2 retrocopies	retro_ogar_1074, retro_ogar_3470,
Pteropus vampyrus	ENSPVAG00000016821	1 retrocopy	retro_pvam_755,
Sarcophilus harrisii	ENSSHAG00000010366	1 retrocopy	retro_shar_622,
Ictidomys tridecemlineatus	ENSSTOG00000001165	2 retrocopies	retro_itri_1273, retro_itri_564,
Tarsius syrichta	ENSTSYG00000002427	1 retrocopy	retro_tsyr_916,