RetrogeneDB ID: retro_cpor_1214

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_57:4569545..4570093(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VRK1
• Ensembl ID: ENSCPOG00000001772
• Aliases: None
• Description: None

Sequence

>retro_cpor_1214
TATTTGAGATCTGGACTATGTAATAAAAATAGAAAATAGTTATAGTCTAGGAAAATAGATCACTTTCAAAGACACCTTAA
GCAAATATATGAAGTGAACACCAAAAGATTTTTCAGAAAACTGTCTTTGAAGTTAAGCCTAAACATTCTGGATGTTGTAG
AGCATATTCATAAACAAGAGGATGTACATGCTGATATCAAAACTTCAAATCTTCGTCTGAGTTACAAGAATCATGCCCAG
GTACATGAGATAGATTATGGCCTACATTGACAGTACTCCTCAGATAAAATTCATAAAGATTATAAAGAAGATATCAAAAG
ATATCTCCATGATGCTAATGAATTCATAAATATTGACATTCACAATGGCATTATCCTACCAAGATAAAAATATAGTGATT
TAGAAATACTGGTTATTGCATGATGCAGTGGCATAGTGTCCATCGTTTTTGGGTAGATAATTTGAAGGATCAAAATTGTG
CTAGAGAATGCAAAATTAGATACCAACACAGTACTGCAATTTTGATAAAGAAGTATTACTTAAAAAAG

Alignment

ORF - retro_cpor_1214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.54 %
• Parental protein coverage: 50.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YWGSGLHDKNGNSYRFMIIDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASN
          Y..SGL..KN........ID.F...L..IYE.N.KRF.RK..L.LSL.ILD..E.IH..E.VH.DIK.SN
Retrocopy YLRSGLCNKNRK*L*SRKIDHFQRHLKQIYEVNTKRFFRKLSLKLSLNILDVVEHIHKQEDVHADIKTSN

Parental  LLLSYKNPDQVYLVDYGLAYRYCPEGVHREYKEDPKRCHDGTIEFTSIDAHHGVAPSR--RGDLEIL-GY
          L.LSYKN..QV...DYGL...Y.....H..YKED.KR......EF..ID.H.G....R....DLEIL.GY
Retrocopy LRLSYKNHAQVHEIDYGLH*QYSSDKIHKDYKEDIKRYLHDANEFINIDIHNGIILPR*KYSDLEIL<GY

Parental  CMIQWLSGHLPWEDNLKDPNYVRDSKIRYRDNIASLMEKCFPEK
          CM.QW.S.H..W.DNLKD.N..R..KIRY....A.L..K....K
Retrocopy CMMQWHSVHRFWVDNLKDQNCARECKIRYQHSTAILIKKYYLKK

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	9.78 RPM
SRP017611_kidney	0.00 RPM	37.90 RPM
SRP017611_liver	0.00 RPM	5.31 RPM
SRP040447_lung	0.00 RPM	14.48 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.84 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1214 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1214 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001772	1 retrocopy	retro_cpor_1214 ,
Danio rerio	ENSDARG00000018006	1 retrocopy	retro_drer_17,
Macropus eugenii	ENSMEUG00000012543	1 retrocopy	retro_meug_186,
Sorex araneus	ENSSARG00000009110	2 retrocopies	retro_sara_287, retro_sara_337,