RetrogeneDB ID: retro_vpac_92

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1734:61409..61720(+)
• Located in intron of: ENSVPAG00000005680

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM17B
• Ensembl ID: ENSVPAG00000009578
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17 homolog B (yeast) [Source:HGNC Symbol;Acc:17310]

Sequence

>retro_vpac_92
GAGGAGTATGAGCGAGAGTTTTGCCCCGGAGAACTGTGGAAGACTGTGGTGGGGCCTTTATGATGGGTACCATAGATAGT
GGTGACTTTCAGGCAATTAAAGGTTTTCACCATTATCCAGTGGGAGTAAACCAGAAACTACAAGGGAGTTTGACAGCTAT
TAAAACCAGGCCTCCACAGTTGGAAGGTGGCTTTACAGTTTAGGGAGGTCTGTCTTCCATGACTGACTGCAGTATGGCTC
ATGTTAGAGGGAAAGAACATCTCTGGAACTCTGTCACAGGTGCTGCCTTTACAGGAGCCATGCCAGCAGCA

Alignment

ORF - retro_vpac_92 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.33 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEYAREPCPW-RIVDDCGGAFTMGVIGGGVFQAIKGFRNAPVGIRHRLRGSV-AVRIR-ALIGXSFAVWG
          EEY.RE.CP..R.V.DCGGAF.MG.I..G.FQAIKGF...PVG....L.GS..A...R.......F.V.G
Retrocopy EEYEREFCPG<RTVEDCGGAFMMGTIDSGDFQAIKGFHHYPVGVNQKLQGSLTAIKTRPPQLEGGFTV*G

Parental  GLFSTIDCGLVRLRGKEDPWNSITSGALTGAVLAA
          GL.S..DC.....RGKE..WNS.T..A.TGA..AA
Retrocopy GLSSMTDCSMAHVRGKEHLWNSVTGAAFTGAMPAA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_92 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_92 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 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,
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 ,