RetrogeneDB ID: retro_vpac_549

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_41335:2590..3212(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000004890
• Aliases: None
• Description: None

Sequence

>retro_vpac_549
AAGGACACAAATGGAGAAGTTCTGTGGGTGTGGTGTTATCCTTGCATGACAGCTACTTTAAGGAATCTGCCGCCGAGAAA
ATGCTGCCTTACAGATGAAAGTAAACTCCGCCCCTTCGTCTTTGGTCAATACAGAAGAACATGGTTTTATACCACAACAG
TTGAAGTTCCAGGTTCTTCCATTTTGAAAAAGGTGACTCATTTTTCTATTGTTCTGACAGCCAAAGATTTTAATCCAGAG
AAATATGCCACCTTCACTAGGGTATTGTGTAGAATGTACCTGAAACACGGGTGCCCTGTTAAGATGACAGAGAGTTACAT
AGCAGTTCTCATGAAGGGGATATGCCAGAGTGAAGAAAATGGCTCTTTTCTCAGCAGGGACTTTGATGCCCAAAAGGCAT
ACCTTGCAGTCTCCATCAAAGACATTGTATCTCAGTTTGGAATGGAAACCATTATCTTAGACACAGCACCGATGATAAAG
AAAAGAATTGTCATCTATCTCCCCAAAATAGAAGCCATCCAGGGGTTTACCAGGACTCTGCCTGTCCTGATGTGACATCA
ACAGGACTGGACCATTCTTCACTCCTTTGTGCACATTTGACACTGATAAGCTGGAAGCCCTG

Alignment

ORF - retro_vpac_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.25 %
• Parental protein coverage: 83.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDTNGEVLWVWCYPSTTATLRNLLLRKCCLTDENKLLHPFVFGQYRRTWFYITTVEVPDSSVLKKVTHFS
          KDTNGEVLWVWCYP..TATLRNL..RKCCLTDE.KL..PFVFGQYRRTWFY.TTVEVP.SS.LKKVTHFS
Retrocopy KDTNGEVLWVWCYPCMTATLRNLPPRKCCLTDESKL-RPFVFGQYRRTWFYTTTVEVPGSSILKKVTHFS

Parental  IVLTAKDFNPEKYAAFTRILCRMYLKHGSPVKMMESYIAVLTKGICQSEENGSFLSKDFDARKAYLAGSI
          IVLTAKDFNPEKYA.FTR.LCRMYLKHG.PVKM.ESYIAVL.KGICQSEENGSFLS.DFDA.KAYLA.SI
Retrocopy IVLTAKDFNPEKYATFTRVLCRMYLKHGCPVKMTESYIAVLMKGICQSEENGSFLSRDFDAQKAYLAVSI

Parental  KDIVSQFGMETVILHTALMLKKRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSYVHL-DADELEAL
          KDIVSQFGMET.IL.TA.M.KKRIV.Y.PKIEA.Q.FTRTLP.L..H.QDWTILHS.VH..D.D.LEAL
Retrocopy KDIVSQFGMETIILDTAPMIKKRIVIYLPKIEAIQGFTRTLPVLM*HQQDWTILHSFVHI>DTDKLEAL

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_549 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_549 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000119979	1 retrocopy	retro_hsap_4757,
Macaca mulatta	ENSMMUG00000008289	1 retrocopy	retro_mmul_411,
Otolemur garnettii	ENSOGAG00000002070	2 retrocopies	retro_ogar_1298, retro_ogar_2990,
Vicugna pacos	ENSVPAG00000004890	1 retrocopy	retro_vpac_549 ,