RetrogeneDB ID: retro_vpac_640

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_900:435268..436020(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSVPAG00000010914
• Aliases: None
• Description: ubiquinol-cytochrome c reductase core protein II [Source:HGNC Symbol;Acc:12586]

Sequence

>retro_vpac_640
CCAGATGAGTTACATTACTATGCTCAGAACCGTTTTACAAGTGCAAGAATGGCTTTGATTGGCCTCCGTGTGAGTCATCC
CCGTTCTAAAAGCAAAGTTGCTAAATGGATCTCAATATGAGGCGTGGGCTTGGTCTATCTGGTGCAAAGGCCAAATACCG
TGGAGGTGAAATTCGAGAACAAAATGGAAACAGTCTCTTCCATGCTGCTCTTGCAGCAGAAAGTGCTGTGACAGGAGTGC
AGCAGCAAATGCATTTAGTGTTCTGCAGCACGTCCTCGGTGCTGAACCACGTTAAGAGGGGCAGCAATGACACCAGCTCT
CTGTACGAGGCTGTTGCCTAGGGAATTCACCAGCCATTTGATGTGTCTGATTTTAATGCCAGTTACTTAGATTCTAGACT
CTTTGGGATTTACACTATCTCACAAGCTGCAGCTGCTGGAGATGTTATCAAGGCTGCCTATAACTAAGTAAAAACAACTG
CTCAAGGAAACCATTCTAACACAGATGTCCAAGCTGCAAAGGACAAGCTGATTGCCGAGTATCTAATGTCAGTGGAGTCT
TCTGGGGGCTTCCTGGATGAAGTCAGGTGCCAGGCTCTAGTTGCTGGTTCATACATGCCACCAGGCAGAGTCCTTCAGCA
GGCTGACTCAGTAGCTGACCCTGATGTCATAAATGCTGCAAAGAAGTTTGTTTCTGGTCAGAAGTCAAAGGCAGCAAGTG
GACATTTGGGGCAGACAACTTTCGTTGATCAG

Alignment

ORF - retro_vpac_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 56.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PDELHHYVQNHFTSARMALIGLGVSH-PVLK-QVAERFLNVRGGLGLSSAKAKYRGGEVREQNGDSLVHA
          PDELH.Y.QN.FTSARMALIGL.VSH.PVLK.Q.....LN.R.GLGLS.AKAKYRGGE.REQNG.SL.HA
Retrocopy PDELHYYAQNRFTSARMALIGLRVSH>PVLK>QSC*MDLNMRRGLGLSGAKAKYRGGEIREQNGNSLFHA

Parental  ALVAESTAAGSAEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVAKGTHQPFDVSAFNASYSDSGLFGIY
          AL.A...A..........V.........HVKRGSN.TSSLY.AVA.G.HQPFDVS.FNASY.DS.LFGIY
Retrocopy AL-AAESAVTGVQQQMHLVFCSTSSVLNHVKRGSNDTSSLYEAVA*GIHQPFDVSDFNASYLDSRLFGIY

Parental  TISQAAAAGDVIKAAYNQVKTIAQGNLSNTDVQTAKNKLKASYLMSVESSESFLDEIGSQALVAGSYVPP
          TISQAAAAGDVIKAAYN.VKT.AQGN.SNTDVQ.AK.KL.A.YLMSVESS..FLDE...QALVAGSY.PP
Retrocopy TISQAAAAGDVIKAAYN*VKTTAQGNHSNTDVQAAKDKLIAEYLMSVESSGGFLDEVRCQALVAGSYMPP

Parental  STVLQQIDAVADADVINAAKKFVSGRKSMAASGNLGHTPFVDE
          ..VLQQ.D.VAD.DVINAAKKFVSG.KS.AASG.LG.T.FVD.
Retrocopy GRVLQQADSVADPDVINAAKKFVSGQKSKAASGHLGQTTFVDQ

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_640 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_640 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.

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640 ,