RetrogeneDB ID: retro_mmus_1509

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:32326183..32326489(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Timm17b
• Ensembl ID: ENSMUSG00000031158
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17b [Source:MGI Symbol;Acc:MGI:1343176]

Sequence

>retro_mmus_1509
GGAGGTCTGTTTTCCACCATCGATTGTGGCCTGGTCCAGCTACGGGGCAAAGAAGACCCCTGGAACTCCGTCACCATTGG
AGCATTGACTGGAGCTGTGTTGGCTGCGCGCAGTGGTCTGCTGGCCATGGTGGGCTCTGCGATGATGGGGCGCATCCTGT
TGGCCCTCATTGAGGGTGTTGGCATCCTCACCTGCTATACTGCCCAGCAGTTCCGCAATGCACCCCCATTCTTGGAGGAC
CCCAGCCAGCTAACCCCTAAAGAGGGATCTCTGGCCCCAGGTTATCCCAACTACCAGCAGTACCAC

Alignment

ORF - retro_mmus_1509 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.26 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGLFSTIDCGLVRLRGKEDPWNSISSGALTGAVLAARSGPLAMVGSAMMGGILLALIEGVGILLTRYTAQ
          GGLFSTIDCGLV.LRGKEDPWNS...GALTGAVLAARSG.LAMVGSAMMG.ILLALIEGVGI.LT.YTAQ
Retrocopy GGLFSTIDCGLVQLRGKEDPWNSVTIGALTGAVLAARSGLLAMVGSAMMGRILLALIEGVGI-LTCYTAQ

Parental  QFRNAPPFLEDPSQLTPKEGSPAPGYPNYQQYH
          QFRNAPPFLEDPSQLTPKEGS.APGYPNYQQYH
Retrocopy QFRNAPPFLEDPSQLTPKEGSLAPGYPNYQQYH

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	0.02 RPM	9.32 RPM
SRP007412_cerebellum	0.09 RPM	8.86 RPM
SRP007412_heart	0.03 RPM	17.59 RPM
SRP007412_kidney	0.02 RPM	15.65 RPM
SRP007412_liver	0.00 RPM	26.05 RPM
SRP007412_testis	0.00 RPM	10.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1509 was not detected

EST

No EST(s) were mapped for retro_mmus_1509 retrocopy.

TSS

No TSS is located nearby retro_mmus_1509 retrocopy 5' end.

Lab

retro_mmus_1509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1509 has 0 orthologous retrocopies within eutheria group .

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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	ENSMMUG00000004547	1 retrocopy	retro_mmul_796,
Mustela putorius furo	ENSMPUG00000013675	1 retrocopy	retro_mputfur_1232,
Mus musculus	ENSMUSG00000031158	1 retrocopy	retro_mmus_1509 ,
Mus musculus	ENSMUSG00000062580	1 retrocopy	retro_mmus_3045,
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,