RetrogeneDB ID: retro_cpor_13

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_72:8716458..8717730(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000022796
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000014629
• Aliases: None
• Description: None

Sequence

>retro_cpor_13
ATGGCGCTCCGAGTCACCCGGAACACAAAAATTAACACTGAAAATAAGGCTACGCTCAGTATGGCAGGCGCTAAGCGTGT
ACCCGTGGCTACTGCAGCAGCCTCCAAGCCAGGTTTGAGGCCAAGAACAGCTCTTGGAGATATCGGTAACAAAGTCAGTG
AGCAGCTGCAAGCCAGAGTGCCTCTGAAAAAGGAAGCAAAAACTTCAGCGACTGGAAAAGTTATGGCTAAAAAACTACAG
AAACCTCTGGAAAAGGTGCCCGTGTGTGTGCCAGAACCAAAACCTGAACCTGAGCCTATTAAGGAAGAAAAACTTTCTCC
TGAACCTATTTTGGTTGACACTCCCTCTCCAAGCCCCATGGAGACCTCTGGCTGCGCTCCTGCAGAAGAAGACCTATGTC
AGGCTTTCTCTGATGTCATTCTGGCTGTGAGTGATGTGGATGCGGAAGATGGAGCAGATCCAAACCTCTGTAGTGAATAT
GTGAAAGATATCTATGCTTATCTCAGGCAGCTTGAGGAAGAGCAGTCAGTCAAACCAAAATACCTGCTGGGTCAAGAGGT
CACTGGAAACATGAGAGCCATCCTAATTGACTGGCTAGTACAGGTTCAGATGAAATTCAGGTTGCTGCAGGAGACTATGT
ACATGACTGTTTCCATTATTGACCGGTTCATGCAGAATAGCTGTGTGCCTAAGAAGATGCTACAGCTGGTTGGAGTCACC
GCCATGTTCATTGCAAGCAAATATGAAGAAATGTACCCTCCAGAAATTGGTGACTTTGCTTATGTGACTAACAGCACTTA
CACTAAGCACCAGATCAGACAGATGGAAATGAAGATTCTCAGAGTTTTGAACTTTGCTCTGGGTCGCCCACTCCCCCTGC
ACTTCCTTCGTAGGGCATCTAAGATTGGAGAGGTTGATGTTGAGCAACATACTTTGGCCAAATACCTGATGGAACTGTCT
ATGTTGGACTATGATATGGTGCACTTTCCTCCTTCTCAAATTGCAGCAGGAGCTTTTTGCTTAGCACTGAAAATTCTTGA
TAATGGTGAATGGACACCAACTCTGCAGCATTACCTGTCGTATACTGAAGAGTCTCTTCTTCCCGTCATGCAGCACCTGG
CTAAGAATATAGTCATGGTGAATCATGGGCTTACGAAGCACATGACTATCAAGAACAAGTATGCTACATCGAAACATGCT
AAGATCAGCACTCTCCCGCAGCTGAACTGTGTATTAGTTAAAGATTTGGCCAAGGCTGTAGCAAAAGTGTAA

Alignment

ORF - retro_cpor_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALRVTRNTKINTENKATLSMAGAKRVPVATAAASKPGLRPRTALGDIGNKVSEQLQARVPLKKEAKTSA
          MALRVTRNTKINTENKATLSMAGAKRVPVATAAASKPGLRPRTALGDIGNKVSEQLQARVPLKKEAKTSA
Retrocopy MALRVTRNTKINTENKATLSMAGAKRVPVATAAASKPGLRPRTALGDIGNKVSEQLQARVPLKKEAKTSA

Parental  TGKVMAKKLQKPLEKVPVCVPEPKPEPEPIKEEKLSPEPILVDTPSPSPMETSGCAPAEEDLCQAFSDVI
          TGKVMAKKLQKPLEKVPVCVPEPKPEPEPIKEEKLSPEPILVDTPSPSPMETSGCAPAEEDLCQAFSDVI
Retrocopy TGKVMAKKLQKPLEKVPVCVPEPKPEPEPIKEEKLSPEPILVDTPSPSPMETSGCAPAEEDLCQAFSDVI

Parental  LAVSDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQSVKPKYLLGQEVTGNMRAILIDWLVQVQMKFRLLQ
          LAVSDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQSVKPKYLLGQEVTGNMRAILIDWLVQVQMKFRLLQ
Retrocopy LAVSDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQSVKPKYLLGQEVTGNMRAILIDWLVQVQMKFRLLQ

Parental  ETMYMTVSIIDRFMQNSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAYVTNSTYTKHQIRQMEMKIL
          ETMYMTVSIIDRFMQNSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAYVTNSTYTKHQIRQMEMKIL
Retrocopy ETMYMTVSIIDRFMQNSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAYVTNSTYTKHQIRQMEMKIL

Parental  RVLNFALGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDYDMVHFPPSQIAAGAFCLALKILDNGE
          RVLNFALGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDYDMVHFPPSQIAAGAFCLALKILDNGE
Retrocopy RVLNFALGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDYDMVHFPPSQIAAGAFCLALKILDNGE

Parental  WTPTLQHYLSYTEESLLPVMQHLAKNIVMVNHGLTKHMTIKNKYATSKHAKISTLPQLNCVLVKDLAKAV
          WTPTLQHYLSYTEESLLPVMQHLAKNIVMVNHGLTKHMTIKNKYATSKHAKISTLPQLNCVLVKDLAKAV
Retrocopy WTPTLQHYLSYTEESLLPVMQHLAKNIVMVNHGLTKHMTIKNKYATSKHAKISTLPQLNCVLVKDLAKAV

Parental  AKV
          AKV
Retrocopy AKV

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	0.69 RPM
SRP017611_kidney	0.00 RPM	3.25 RPM
SRP017611_liver	0.04 RPM	0.87 RPM
SRP040447_lung	0.03 RPM	4.44 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.68 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_13 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_13 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 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000013401	1 retrocopy	retro_cpor_1278,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13 ,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Myotis lucifugus	ENSMLUG00000012856	1 retrocopy	retro_mluc_1020,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,
Tursiops truncatus	ENSTTRG00000002874	2 retrocopies	retro_ttru_524, retro_ttru_59,