RetrogeneDB ID: retro_cpor_701

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:26955583..26956360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUS4L
• Ensembl ID: ENSCPOG00000002384
• Aliases: None
• Description: None

Sequence

>retro_cpor_701
GTTATAGCCACTGATTTTATCAGATCCATAAAAGCCAGAGACAGTGAATTTACTACCACTAACCAAGGTGATTGCCCATT
GATTGTGCAGTTTGCTGCTAATGATGCAAGACTTTTATCTGATGCTGCTCACAAACTGTGTCCTTATGCGAATGGAATAG
GCATGAACTGTGGTTGCTCGCAGAGGTGGCTGATCATGGAAGGTTATGGACTTGCTTAATAAACAGGCCAAACTTTGTTT
GAGGTACAGTGAAACAAGTAAGAAATCAAGTGGAAAACCCCAGATTTTCAGTTCCTATTAAAATAAGGTCCATGATGACC
TTACAAAGAACTGTAAACTTTTGTCAACAGTCTGAAGCAGCAAGAGTTAACTGGATTACAGGCCATGGAAGAACTGCTGA
AGGAAGACATCAGCCAGTCCAGAATGATGCCATTAGAATACTAAAGGAAACATGTCCTTATCTGTGATTGTTAATGGAGA
CATCATAAGATTTAAAAAAACAGAAAATGTGTGGCAAGTTATGGGACAGATGGCATGATGGTTGCAAGGGGACTCTTGGT
GAACCCTGCCGTGCTTGCTGGATGTGAGGGAAACCCACTGAAATGCGTCTGGGACCGGGTGGACATCACTCTTGAACTTG
GGACTTCTTTTGTTTGTTTCCATCAACATTTAATGCACCTGATGGAAAAAATAACTTCAAGGTAAGAAAAAAGAATATTT
AAGTGTCTGTTAAGCACATCAGCAGGTTTAGATTACCTTATAGACCATTATGACATT

Alignment

ORF - retro_cpor_701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 81.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IVAADFVRSIKARDSEFTT-NQGDCPLIVQFAANDARLLSDAARIVCPYANGIDINCGCPQRWAMAEGYG
          ..A.DF.RSIKARDSEFTT.NQGDCPLIVQFAANDARLLSDAA...CPYANGI..NCGC.QRW...EGYG
Retrocopy VIATDFIRSIKARDSEFTTTNQGDCPLIVQFAANDARLLSDAAHKLCPYANGIGMNCGCSQRWLIMEGYG

Parental  -ACLINKPELVRDMVKQVRNQVENPRFSVSIKIR-IHDDLT-RTVDFCRKAEATGVNWITVHGRTVEERH
          ..CLIN.P..V...VKQVRNQVENPRFSV.IKIR..HDDLT.RTV.FC...EA..VNWIT.HGRT.E.RH
Retrocopy <TCLINRPNFV*GTVKQVRNQVENPRFSVPIKIR<VHDDLT>RTVNFCQQSEAARVNWITGHGRTAEGRH

Parental  QPVHYDAIKIIKE-NMSIPVIANGDIRSLKEAENVWQITG-TDGVMVARGLLANPAMFAGYEETPLKCIW
          QPV..DAI.I.KE.NMS..VI.NGDI...K..ENVWQ..G.TDG.MVARGLL.NPA..AG.E..PLKC.W
Retrocopy QPVQNDAIRILKE<NMSLSVIVNGDIIRFKKTENVWQVMG<TDGMMVARGLLVNPAVLAGCEGNPLKCVW

Parental  DWVDIALELGTPFMCFHQHLMYMMEKITSKQEKRIFNALSSTSAVLDYLTDHYGI
          D.VDI.LELGT.F.CFHQHLM..MEKITS..EKRIF..L.STSA.LDYL.DHY.I
Retrocopy DRVDITLELGTSFVCFHQHLMHLMEKITSR*EKRIFKCLLSTSAGLDYLIDHYDI

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	0.12 RPM	2.24 RPM
SRP017611_kidney	0.00 RPM	1.99 RPM
SRP017611_liver	0.00 RPM	2.48 RPM
SRP040447_lung	0.00 RPM	3.51 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.48 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_701 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_701 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006848	1 retrocopy	retro_chof_1283,
Cavia porcellus	ENSCPOG00000002384	1 retrocopy	retro_cpor_701 ,
Otolemur garnettii	ENSOGAG00000013113	2 retrocopies	retro_ogar_1578, retro_ogar_894,