RetrogeneDB ID: retro_cpor_405

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_142:1803972..1804560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC3
• Ensembl ID: ENSCPOG00000008739
• Aliases: None
• Description: None

Sequence

>retro_cpor_405
TTGATTTTGTGCTGCAATTCTACATCTGAAGTGATATCTCCTATTCATAGTAGGTGCCTAGCAGTTCATGTGCCTGTTCA
CATCATTCAAGATATTTGCCGTATGTTATCTACTGTATACAAAAAGCAAGGTCTGAGTTTCCCTTCACAGTTGGCTCAGA
GAATTGCAGAAAAATCCTGCATAAATCTCAGAAAAAAACTGCTTAAGTGCAAAGCTTGCAGAGTGCAAAAGTATCCTTTT
ACTGTAGATGAAGAAATCCCTGAGACAGATTGGGGGGTTTATCTGGGCGAGATGGCAAATACTATTTTCAGTCAACAGAT
GCCACAGTGACTTCTTGATGTTTATGGAATGCTGTATGAGCTTTTTACTCATTATATTCCTCTGGAGATAATAATGAAGG
GCCTGTTCTGAGAACTTTTACACAATTATGATGGAAAACTGAAAAGGGAAGTTACCTAGCGGATGGTTTATTATGAACAT
TGTCTACAGCTGGGTAACAAAGCCATATATCACTTGGAAGCATTTGTGGCCAAATTTATGTCACTTTATAAGAAATTCAT
GAAGGACGAAGTGGAAAGCATGATGTTC

Alignment

ORF - retro_cpor_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.84 %
• Parental protein coverage: 70.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLCKDSNTTTLMEVRNQNLKQQSFFNIINQICHVLSTVCKKEGLSLPSQLAQRIAEKSCRNLRKALLMC
          L.LC..S............L.......II..IC..LSTV.KK.GLS.PSQLAQRIAEKSC.NLRK.LL.C
Retrocopy LILCCNSTSEVISPIHSRCLAVHVPVHIIQDICRMLSTVYKKQGLSFPSQLAQRIAEKSCINLRKKLLKC

Parental  EACRVQQYPFTADQEIPETDWEVYLRETANAIVSQQTPQRLLEVRGRLYELLTHCIPPEIIMKGLLSELL
          .ACRVQ.YPFT.D.EIPETDW.VYL.E.AN.I.SQQ.PQ.LL.V.G.LYEL.TH.IP.EIIMKGL..ELL
Retrocopy KACRVQKYPFTVDEEIPETDWGVYLGEMANTIFSQQMPQ*LLDVYGMLYELFTHYIPLEIIMKGLF*ELL

Parental  HNCDGQLKGEVTQMAAYYEHRLQLGTKAIYHLEAFVAKFMALYKKFMEDGLEGMMF
          HN.DG.LK.EVT....YYEH.LQLG.KAIYHLEAFVAKFM.LYKKFM.D..E.MMF
Retrocopy HNYDGKLKREVT*RMVYYEHCLQLGNKAIYHLEAFVAKFMSLYKKFMKDEVESMMF

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	4.14 RPM
SRP017611_kidney	0.00 RPM	2.30 RPM
SRP017611_liver	0.00 RPM	1.35 RPM
SRP040447_lung	0.00 RPM	3.61 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_405 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_405 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018380	1 retrocopy	retro_cjac_1611,
Cavia porcellus	ENSCPOG00000008739	1 retrocopy	retro_cpor_405 ,
Myotis lucifugus	ENSMLUG00000014088	1 retrocopy	retro_mluc_1754,
Mustela putorius furo	ENSMPUG00000001885	1 retrocopy	retro_mputfur_1073,
Nomascus leucogenys	ENSNLEG00000001169	1 retrocopy	retro_nleu_674,
Pongo abelii	ENSPPYG00000005272	1 retrocopy	retro_pabe_2420,
Tupaia belangeri	ENSTBEG00000004725	1 retrocopy	retro_tbel_4191,
Tarsius syrichta	ENSTSYG00000009501	2 retrocopies	retro_tsyr_1772, retro_tsyr_331,