RetrogeneDB ID: retro_vpac_512

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_2788:93312..93809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL45
• Ensembl ID: ENSVPAG00000004977
• Aliases: None
• Description: mitochondrial ribosomal protein L45 [Source:HGNC Symbol;Acc:16651]

Sequence

>retro_vpac_512
GCAGCCCCCATGCCGGGGGAGGTTGTCTTACTTATCCAGAGCTTCTGAATAGTGGTCTCTGTGGTCAGTCCTGGTGACTC
AGTACACAGCTGTGAGAACTAAAACACATTTCACACCCCCTATTTTTGAACCCAAATACAAATCAGAAAAAGGCGTTTAT
AGAATGTGCTGGGAAAGCAGGACTGGCCATGCCTCTGGAACATTTGGCGCATCCCGTGCACCTGGCCTGTAGAGCTGGTA
TCTTTGACACCTGTATTCCTCCTGAGGGTAATGCGCTCATGTCATCTCTTTCAAAGAAAGGACTGACACAGAGAACTGAG
CAGCTGAAGAAGAATGTAGCTTCACAATTGTCCATTCAGAAGGTAAAAGAATATGATGCTAATTTGAAAACAAAGGACTT
CCCTGAGAAAGCTGAGGCTATCTTTATTGATGCTCACCTTTTTCTAAACAATTTAGATCATGATCAGCTTCATAGCTTGG
TAATTGATAACTGTTTC

Alignment

ORF - retro_vpac_512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 54.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAPMPRG-LSCLSRALGWWSWQPVLVTQSTTVVPVRTKKRFTPPAYKPKYKSEK-EFIEYARKAGLVIPP
          AAPMP...LS.LSRA...WS...VLVTQ.T....VRTK..FTPP...PKYKSEK..FIE.A.KAGL..P.
Retrocopy AAPMPGE>LSYLSRASE*WSLWSVLVTQYTA---VRTKTHFTPPIFEPKYKSEK>AFIECAGKAGLAMPL

Parental  ERLERPIHLACTAGIFDAYVPPEGDARISSLSKEGLAQRTERLKKNVASQLSIRKIKESDPNFKIKDFPE
          E.L..P.HLAC.AGIFD...PPEG.A..SSLSK.GL.QRTE.LKKNVASQLSI.K.KE.D.N.K.KDFPE
Retrocopy EHLAHPVHLACRAGIFDTCIPPEGNALMSSLSKKGLTQRTEQLKKNVASQLSIQKVKEYDANLKTKDFPE

Parental  KAKDIFIEAHLCLNNSDHDRLHTLVTENCF
          KA..IFI.AHL.LNN.DHD.LH.LV..NCF
Retrocopy KAEAIFIDAHLFLNNLDHDQLHSLVIDNCF

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_512 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_512 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000005808	2 retrocopies	retro_fcat_1677, retro_fcat_283,
Monodelphis domestica	ENSMODG00000012560	1 retrocopy	retro_mdom_403,
Nomascus leucogenys	ENSNLEG00000000530	1 retrocopy	retro_nleu_1967,
Otolemur garnettii	ENSOGAG00000015816	1 retrocopy	retro_ogar_1029,
Pan troglodytes	ENSPTRG00000009065	1 retrocopy	retro_ptro_107,
Ictidomys tridecemlineatus	ENSSTOG00000000304	2 retrocopies	retro_itri_102, retro_itri_1575,
Tupaia belangeri	ENSTBEG00000000585	1 retrocopy	retro_tbel_4621,
Vicugna pacos	ENSVPAG00000004977	1 retrocopy	retro_vpac_512 ,