RetrogeneDB ID: retro_cpor_1107

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_46:12821179..12822122(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSCPOG00000008824
• Aliases: None
• Description: None

Sequence

>retro_cpor_1107
CTGGCTCAACTCCAGACATGCTTCCTCACAGACAGTAAGAAACATGGAGTAGATGATGTTCCCTTCCCAATCCCTGACAG
CTCTGAAATTGCTGACCTTAGTAATACCATAAATAAATTGCTAGAGGCCAAAAATAAGTTCCACAAATATGTGGCGCTTC
ATTTCCTTATCAATGGCCAGTTTTCATGAATGCCATTGGCCAAGCACATGGAAGTGGAAAATATCTCATTAGAAGTTGTG
AAACTAGAATATGTGGAAAAGTGTACTGCTGCCCAATCAGAGCAGTGCATGTTCCATGATAACTGGATCAGCTCAGTGTC
AAAGGGTCAAAACAATCAATTTTGACTGGTTCTCATGATAAGACTTCTCCAATATAGTCTTTTGAAGGAACATGAATAAT
GATAAATGTGGAGCATACATATGTTTTGGAAGATATAGCCTGTGTAAAAAAAAGTTTGAGGTGCTTACTATGAGTCCCTC
TATGGATCAGACTTTTCTCCTATGGGAATGGAGTGTAGAGAGAAATAAAATAAAAGCTGTACACTGCTGTAGCGGCCATG
TAGGAAGTATGGATTCTATAGCAGTTGAAAACTCTGGAATTAAATTTTTCCGTGGTTCCTGGGATAAGATGCTAAAGATC
TGATCCGCAGTCCCAACAGATGAAGAAGACAAAATGGAGGAATCCAGAAATTGATGAAGAAAGAAACAGAAAACAGAGTA
TTTAGGATTAACAAGGGCTCCCATGGTGACCCTCTCTGACCACACAGAAGCAATTTCTTCAGTACTGTGGGCAGATGCTG
AAGAAATCTGCAGTGCATCTTGGGACCACACAATTAGAATGTGGGATGTTGAGTCTGGCTGTCTTAAGTCAACTTTGACA
GGTAATAAAATGTTTAATTGTATTTCCTATTCTCCACTCTGTATACATCTAACAACTGGCAGC

Alignment

ORF - retro_cpor_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.61 %
• Parental protein coverage: 74.7 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQLQTRFFTDNKKYAVDDVPFSIPASSEIADLSNIINKLLEAKNEFHKYVEFDFLIKGQFLRMPLAKHM
          .AQLQT.F.TD.KK..VDDVPF.IP.SSEIADLSN.INKLLEAKN.FHKYV...FLI.GQF..MPLAKHM
Retrocopy LAQLQTCFLTDSKKHGVDDVPFPIPDSSEIADLSNTINKLLEAKNKFHKYVALHFLINGQFS*MPLAKHM

Parental  EVENISSEEVVELEYVEKYTAPQPEQCMFHDDWVSAV-KG-AEEWILTGSYDKTSRIWSLEGTSIMTIVG
          EVENIS..EVV.LEYVEK.TA.Q.EQCMFHD.W.S.V.KG.....ILTGS.DKTS.I.S.EGT.IM..V.
Retrocopy EVENISL-EVVKLEYVEKCTAAQSEQCMFHDNWISSVSKG<SKQSILTGSHDKTSPI*SFEGT*IMINVE

Parental  HTDVVKDVAWVKKDSLSCLL-LSASMDQTILLWEWSVERNKVKALHCCRGHAGSVDSIAVDSSGTKFCSG
          HT.V..D.A......L.CLL..S.SMDQT.LLWEWSVERNK.KA.HCC.GH.GS.DSIAV..SG.KF..G
Retrocopy HTYVLEDIA-CXXXXLRCLL<MSPSMDQTFLLWEWSVERNKIKAVHCCSGHVGSMDSIAVENSGIKFFRG

Parental  SWDKMLKIWSAVPTDEEDEMEESTNRPRKKQKTEQLGLTRTPIVTLSGHTEAISSVLWSDAEEICSASWD
          SWDKMLKI.SAVPTDEED.MEES.N..RKKQKTE.LGLTR.P.VTLS.HTEAISSVLW.DAEEICSASWD
Retrocopy SWDKMLKI*SAVPTDEEDKMEESRN**RKKQKTEYLGLTRAPMVTLSDHTEAISSVLWADAEEICSASWD

Parental  HTIRVWDVESGSLKSTLTGNKVFNCISYSPLCKRLASGS
          HTIR.WDVESG.LKSTLTGNK.FNCISYSPLC..L..GS
Retrocopy HTIRMWDVESGCLKSTLTGNKMFNCISYSPLCIHLTTGS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	18.29 RPM
SRP017611_kidney	0.00 RPM	16.85 RPM
SRP017611_liver	0.00 RPM	11.67 RPM
SRP040447_lung	0.00 RPM	13.64 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1107 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1107 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107 ,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,