RetrogeneDB ID: retro_cpor_570

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:14476770..14477123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSCPOG00000019520
• Aliases: None
• Description: None

Sequence

>retro_cpor_570
ATGGCTGAACTGATTCAAAAGAAACTGCAGAGGGAAGTGGAGAAATATCAACAACTACAGAAGGACTTGAGTAAATTCAT
GTTGGGGAGAAAGAAGCTTGAGGCACAACTAACAGGAAATAGTATTTTGAAGGAGGAACTGACACTGCTGAATGGTCCAG
TGTGGGTCTTCACACTTCTGGGTTCTTTGCTAGTCAAACAGGAGATGGGGAGGCTCAGGCCACAGAGGAGATGTTGGACT
ATATTGCAGCTGAAATGAAGCAATATGAACCCCAGATCCAGGACTTCTAGTGGTAATCAAAACAACAGAGGGAGATACTT
GGTCAGCTATAAGAGGTGTTCTGGCAGGTCCAG

Alignment

ORF - retro_cpor_570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.83 %
• Parental protein coverage: 90.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQEL-
          MAELIQKKLQ.EVEKYQQLQKDLSK.M.GR.KLEAQLT.N.I.KEEL.LL.G...VF.LLG..LVKQE..
Retrocopy MAELIQKKLQREVEKYQQLQKDLSKFMLGRKKLEAQLTGNSILKEELTLLNGPVWVFTLLGSLLVKQEM<

Parental  GEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFRRAQ
          GEA.AT....LDYI.AE.K.YE.Q..D....S.QQRE.L.QL...F...Q
Retrocopy GEAQAT-EEMLDYIAAEMKQYEPQIQDF*W*SKQQREILGQL*EVFWQVQ

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	18.92 RPM
SRP017611_kidney	0.00 RPM	18.32 RPM
SRP017611_liver	0.00 RPM	18.24 RPM
SRP040447_lung	0.00 RPM	11.55 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_570 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_570 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570 ,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216, retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454,