RetrogeneDB ID: retro_cpor_308

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:41132954..41133445(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C21ORF91
• Ensembl ID: ENSCPOG00000012714
• Aliases: None
• Description: None

Sequence

>retro_cpor_308
AAGCCAGATGAAAAATTACTCCCACAGTTTGATTCCGAAGTACCAAAATATTCTGCAAGATGGTTAGATAGAAGTACTAG
TGGCATCTCAAACTGTACACAATGAATTTTGAAGCAGATAAAAAATACAGACCTTGGACTTGCTATGTTACAAGGTCTAG
GTGCCACTTTACGCCATGACAGTGTTTTGTGGTCTCGTACTCACAGCCAGACACAGAAAAAAGAAGTGGCCATTTTCTTC
CCTGAAGCTTATGTCCAAATTCAGACTCTGCATTTACAGCAGAGAGGAATTGAACTGAATGATCTTGATGAAGTAGAACT
GAATATAAAATTTTGACAGCAAATCAGGAAGTTTTTGAAGAGTTAATACATCAAATACACGAAAAAGATTCTCTGACATC
ACAGTGTTGAGTCCACCACGTTGCCACTGAACAGCTTCACAAGAACTGCTCCAAGTTACCATGCCTGTAAGTAGGACAAA
CAGAAGCAAAC

Alignment

ORF - retro_cpor_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.05 %
• Parental protein coverage: 54.39 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KPDKKLLPQFDSQVPKYSARWIDGSTSGISNCTQEILEQRKNTDFGLAVLQGPGAALCHDNVLW--PHAQ
          KPD.KLLPQFDS.VPKYSARW.D.STSGISNCTQ.IL.Q.KNTD.GLA.LQG.GA.L.HD.VLW...H.Q
Retrocopy KPDEKLLPQFDSEVPKYSARWLDRSTSGISNCTQ*ILKQIKNTDLGLAMLQGLGATLRHDSVLWSRTHSQ

Parental  GQ--EEATFCPEANVPTQTLR-YSREELNSM-TLDEVKQLNTKLRQQI-QDVFEELTHQVQEKDSLISER
          .Q..E.A.F.PEA.V..QTL..YSREELN.M..LDEV..LN.K..QQI.Q.VFEEL.HQ..EKDSL.S..
Retrocopy TQKKEVAIFFPEAYVQIQTLH>YSREELN*M<DLDEV-ELNIKF*QQI<QEVFEELIHQIHEKDSLTSQC

Parental  HGRHVAIEQLHKNCSKLPCLQVGRTGTN
          ...HVA.EQLHKNCSKLPCL.VG.T..N
Retrocopy *VHHVATEQLHKNCSKLPCL*VGQTEAN

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	4.20 RPM
SRP017611_kidney	0.00 RPM	1.36 RPM
SRP017611_liver	0.00 RPM	3.40 RPM
SRP040447_lung	0.00 RPM	3.05 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.15 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_308 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_308 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012714	1 retrocopy	retro_cpor_308 ,