RetrogeneDB ID: retro_vpac_296

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_471:1268120..1268553(-)
• Located in intron of: ENSVPAG00000011685

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA3
• Ensembl ID: ENSVPAG00000009784
• Aliases: None
• Description: cell division cycle associated 3 [Source:HGNC Symbol;Acc:14624]

Sequence

>retro_vpac_296
CCTTCATCTAAATTGAAATTGCCCTCAGGCACCAGTTATCCCCTGAGGACCAGACAGCACCCTGGAGCCAGACTGAGCTT
CCTTCCAAGGTGTTTTCCAAGGAGGAAACAGGACAGCACACAGAAACCGCTATGGCCAGCCAGGGCTCAGGCAAGCCCTT
GAGAGACCTCTAGCCTCCCTGATCTTCAGGTTCTAAGCACAAGAGATGGAAATCAAACAGCAGAGTACCAGGGAGATCTC
CACTCACCACCCTATAGGAGGACAACTCCCCCAGGATCCTGACACCACAGCAGGGTAAGCAGCCCTCTCCCCTAAGTGAA
AATACTAGGGAACTAAAGGAAGGGGCCACTCTGGAAACTGCGTGACTTCTAAAAACTGGAGGCAAGCTTGGGAGCAAGGC
CAGGACCATAACAAGGGAAATCAGCACTTCCCT

Alignment

ORF - retro_vpac_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.22 %
• Parental protein coverage: 79.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSSQLDLP-LDSQFSLEDQMSPWSQTELPSKQVFSKEETGQSSGTPVGSQGSDKPLRDPETPRSPGSMRS
          PSS.L.LP.L..Q.S.EDQ..PWSQTELPSK.VFSKEETGQ...T...SQGS.KPLRD...P.S.GS...
Retrocopy PSSKLKLP<LRHQLSPEDQTAPWSQTELPSK-VFSKEETGQHTETAMASQGSGKPLRDL*PP*SSGSKHK

Parental  RWKPNSKVLGRSPLTILQDDNSPGTLTPRQSKRPSPLSENIKELKGGAVLGTGRLPKTGGR-AWEQGQGH
          RWK.NS.V.GRSPLT.L..DNSP..LTP.Q.K.PSPLSEN..ELK.GA.L.T..L.KTGG..AWEQGQ.H
Retrocopy RWKSNSRVPGRSPLTTL*EDNSPRILTPQQGKQPSPLSENTRELKEGATLETA*LLKTGGK<AWEQGQDH

Parental  DKENRHFP
          .K.N.HFP
Retrocopy NKGNQHFP

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_296 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_296 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013985	1 retrocopy	retro_amel_1158,
Canis familiaris	ENSCAFG00000014650	4 retrocopies	retro_cfam_1100, retro_cfam_1940, retro_cfam_345, retro_cfam_633,
Cavia porcellus	ENSCPOG00000012334	1 retrocopy	retro_cpor_1073,
Felis catus	ENSFCAG00000004274	2 retrocopies	retro_fcat_1182, retro_fcat_1942,
Mustela putorius furo	ENSMPUG00000016781	1 retrocopy	retro_mputfur_663,
Pteropus vampyrus	ENSPVAG00000012300	4 retrocopies	retro_pvam_235, retro_pvam_248, retro_pvam_297, retro_pvam_667,
Rattus norvegicus	ENSRNOG00000015529	1 retrocopy	retro_rnor_2685,
Ictidomys tridecemlineatus	ENSSTOG00000023573	1 retrocopy	retro_itri_804,
Tupaia belangeri	ENSTBEG00000001905	1 retrocopy	retro_tbel_534,
Vicugna pacos	ENSVPAG00000009784	1 retrocopy	retro_vpac_296 ,