RetrogeneDB ID: retro_vpac_177

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2435:410449..411023(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSVPAG00000011480
• Aliases: None
• Description: zinc finger, DHHC-type containing 4 [Source:HGNC Symbol;Acc:18471]

Sequence

>retro_vpac_177
ATGGACTTCCTCTTTCTCTTCTTGTTCTACCTGACTTCGGTGCTGATTGGTGGTGTTCTGATCTGCATCTGCTCAAAAAC
ACATTGCTTGAAAGGCCTGGTCGGAAGAGGAACACAGGTATTTTCCTATATAATCCCAGAATGCCTTCAGAGAGCCATGC
TAAAATTGTTTCATTACCTCTTCCATACACGAAACCACACCTTCATTATCCTGCACCTCATCTTGCAAGGGATGATTTAT
ACTCAATACACTTGGGAAATACTTGGCTACTGTCGAGAGCTCGAGTTCTTCCTGTATTACCTCCTTCTGCCTTATCTGCT
GCTGATTATAAACCTGATTTTTTTCACCCTGAGTTGTGTGACTAACCCTGGTACCAATAACAAAAGCAAACGAATTACTG
CTGCTTCAAGTTTATGAATTCGATGAAGTGATGTTCCCCAAGAACATGAGATGCTCTACTTGTGATTTAAGGAAACCAGC
ACGATCCAAGCACTGCAGTGTGTGTAACCGGTGTGTGCACCGCTTTGACCATCACTGTGTGTGGGTGAACAACTGCATCG
GGGCCTGGAACACC

Alignment

ORF - retro_vpac_177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.88 %
• Parental protein coverage: 54.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDFLFLFLFYLASVLIGVVLICICSKTHCLKGLVGRGTQVFSYIIPECLQRAMLKLLHYLFHTRNHTFII
          MDFLFLFLFYL.SVLIG.VLICICSKTHCLKGLVGRGTQVFSYIIPECLQRAMLKL.HYLFHTRNHTFII
Retrocopy MDFLFLFLFYLTSVLIGGVLICICSKTHCLKGLVGRGTQVFSYIIPECLQRAMLKLFHYLFHTRNHTFII

Parental  LHLILQGMIYTEYTWEILGYCRELEFSLYYLLLPYLLLIINLIFFTLSCVTNPGT-ITKANELLLLQVYE
          LHLILQGMIYT.YTWEILGYCRELEF.LYYLLLPYLLLIINLIFFTLSCVTNPGT.ITKANELLLLQVYE
Retrocopy LHLILQGMIYTQYTWEILGYCRELEFFLYYLLLPYLLLIINLIFFTLSCVTNPGT>ITKANELLLLQVYE

Parental  FDEVMFPKNMRCSTCDLRKPARSKHCSVCNRCVHRFDHHCVWVNNCIGAWNT
          FDEVMFPKNMRCSTCDLRKPARSKHCSVCNRCVHRFDHHCVWVNNCIGAWNT
Retrocopy FDEVMFPKNMRCSTCDLRKPARSKHCSVCNRCVHRFDHHCVWVNNCIGAWNT

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_177 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_177 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009547	1 retrocopy	retro_btau_643,
Dasypus novemcinctus	ENSDNOG00000009165	1 retrocopy	retro_dnov_2610,
Homo sapiens	ENSG00000136247	1 retrocopy	retro_hsap_1193,
Macaca mulatta	ENSMMUG00000015545	1 retrocopy	retro_mmul_1283,
Nomascus leucogenys	ENSNLEG00000015607	1 retrocopy	retro_nleu_2081,
Pongo abelii	ENSPPYG00000017352	1 retrocopy	retro_pabe_993,
Pan troglodytes	ENSPTRG00000018915	1 retrocopy	retro_ptro_3038,
Pteropus vampyrus	ENSPVAG00000016104	2 retrocopies	retro_pvam_1175, retro_pvam_758,
Ictidomys tridecemlineatus	ENSSTOG00000011605	1 retrocopy	retro_itri_1054,
Tursiops truncatus	ENSTTRG00000005001	1 retrocopy	retro_ttru_179,
Vicugna pacos	ENSVPAG00000011480	1 retrocopy	retro_vpac_177 ,