RetrogeneDB ID: retro_mmul_796

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:17825484..17825987(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000023723
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TIMM17B
• Ensembl ID: ENSMMUG00000004547
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17 homolog B (yeast) [Source:HGNC Symbol;Acc:17310]

Sequence

>retro_mmul_796
ATGGAGGAGTACGCCTGGGAGCCTTGCCCATGGCGAATTGTGGATGATTGTGGTGGAGTCTTCACTGTGGGTGTCATCGG
TGGTGGAGTCTTCCAGGCCATCAAGGGTTTCTGCAATGCCCCTGTTGGAATTCGGCACCAGTTGAGAGGTAGTGCCAACA
CTGTGAGGATCCAAGTCTCCCAGATTGGAGGTAGCTTTGCAGTGTTGGGGGTCTTGTTCTCCACCATGGACTGTGGCCTG
GTACAGCTTCAGGGCAAGGAGGATCCCTGGAAATCTATCACCAGTGGAGTATTGATGGGGCTGTGCTGACTGCCTGCAGT
GGCCCACTGGCCATGGTGGCCTCAGCGATGATGGGGGACATCCTGTTGGCCCTCATTGAGGGTGTTGGCATCCTCCTCAC
TCGCTACACAGCCCAGCAGTTCCAAAATGCTCCCTCATTCCTGGAGGACCCAAGCCAACTGCCCCCTAAGGACGTTACCC
AGGCCCCAGGCTATCCCATATAT

Alignment

ORF - retro_mmul_796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.43 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEEYAREPCPWRIVDDCGGAFTMGVIGGGVFQAIKGFRNAPVGIRHRLRGSTNAVRIRAPQIGGSFAVWG
          MEEYA.EPCPWRIVDDCGG.FT.GVIGGGVFQAIKGF.NAPVGIRH.LRGS.N.VRI...QIGGSFAV.G
Retrocopy MEEYAWEPCPWRIVDDCGGVFTVGVIGGGVFQAIKGFCNAPVGIRHQLRGSANTVRIQVSQIGGSFAVLG

Parental  GLFSTIDCGLVRLRGKEDPWNSITSGAL-TGAVLAARSGPLAMVGSAMMGGILLALIEGVGILLTRYTAQ
          .LFST.DCGLV.L.GKEDPW.SITSG.L..GAVL.A.SGPLAMV.SAMMG.ILLALIEGVGILLTRYTAQ
Retrocopy VLFSTMDCGLVQLQGKEDPWKSITSGVL<DGAVLTACSGPLAMVASAMMGDILLALIEGVGILLTRYTAQ

Parental  QFRNAPPFLEDPSQLPPKDGTPAPGYPSY
          QF.NAP.FLEDPSQLPPKD.T.APGYP.Y
Retrocopy QFQNAPSFLEDPSQLPPKDVTQAPGYPIY

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
SRP007412_brain	0.00 RPM	4.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.01 RPM
SRP007412_cerebellum	0.00 RPM	4.20 RPM
SRP007412_heart	0.00 RPM	9.54 RPM
SRP007412_kidney	0.00 RPM	8.10 RPM
SRP007412_liver	0.00 RPM	12.27 RPM
SRP007412_testis	0.00 RPM	4.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_796 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_796 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_974
Pan troglodytes	retro_ptro_671
Gorilla gorilla	retro_ggor_779

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012474	1 retrocopy	retro_amel_717,
Bos taurus	ENSBTAG00000018496	4 retrocopies	retro_btau_1022, retro_btau_1550, retro_btau_1552, retro_btau_882,
Cavia porcellus	ENSCPOG00000008768	2 retrocopies	retro_cpor_867, retro_cpor_893,
Dasypus novemcinctus	ENSDNOG00000025897	2 retrocopies	retro_dnov_2282, retro_dnov_2406,
Felis catus	ENSFCAG00000002569	2 retrocopies	retro_fcat_1429, retro_fcat_1654,
Gorilla gorilla	ENSGGOG00000011427	1 retrocopy	retro_ggor_779,
Macropus eugenii	ENSMEUG00000004174	1 retrocopy	retro_meug_2071,
Microcebus murinus	ENSMICG00000005971	3 retrocopies	retro_mmur_1128, retro_mmur_1272, retro_mmur_232,
Myotis lucifugus	ENSMLUG00000009148	1 retrocopy	retro_mluc_148,
Macaca mulatta	ENSMMUG00000001924	1 retrocopy	retro_mmul_562,
Macaca mulatta	ENSMMUG00000004547	1 retrocopy	retro_mmul_796 ,
Mustela putorius furo	ENSMPUG00000013675	1 retrocopy	retro_mputfur_1232,
Mus musculus	ENSMUSG00000031158	1 retrocopy	retro_mmus_1509,
Nomascus leucogenys	ENSNLEG00000007902	1 retrocopy	retro_nleu_1616,
Oryctolagus cuniculus	ENSOCUG00000027418	2 retrocopies	retro_ocun_121, retro_ocun_1451,
Pteropus vampyrus	ENSPVAG00000007643	1 retrocopy	retro_pvam_470,
Ictidomys tridecemlineatus	ENSSTOG00000014173	1 retrocopy	retro_itri_83,
Tarsius syrichta	ENSTSYG00000010396	2 retrocopies	retro_tsyr_1132, retro_tsyr_1703,
Vicugna pacos	ENSVPAG00000009578	1 retrocopy	retro_vpac_92,