RetrogeneDB ID: retro_cpor_870

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_30:22206994..22207463(+)
• Located in intron of: ENSCPOG00000000935

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000022086
• Aliases: None
• Description: None

Sequence

>retro_cpor_870
GACAAACTGAAATCACTGCAGAAGGATGAAGTATAGCAGTTTATGAGCTTTAAAGAATCTACTAAAAAAAATTGTAGCAA
GTTGTCTTTCTCAAAATGACTGCAAGTTAGATACTGCAACAAATAATATTTTCCAAAATCCTGAACTTTATATACAAGAG
AGTATAAAAGGATCATTGAATGGGAAGATGTTTGAACAGCTATACAACAGATACAAACATCCTCAAGCTGAAAATAAAAC
TAGAATGGATGGCATACAATAGTTCTGTGATGACCTGGACTCGACCAAGCCAGCATTAGTGCTGGGATCACTGCACGAAT
TTCAGAGGGCAACACTATGTGAGTCCTCCAAACAGGAGTTTGTGGACAGCGTGACAGATCTAGGATGAGCCAGCAGAGAA
AAGCTAAAGGCTCAAATACCAAAGATGCAACCAGAATTCTAAGAACAAGAATGATTTAAGGATGTTTTT

Alignment

ORF - retro_cpor_870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.86 %
• Parental protein coverage: 60.85 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSEKTA-VSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYN
          .KLKS.QKD.V.QFM.F..S.......SCLSQND.KLD.AT.N.FQNPELYI.ES.KGSL..K..EQLYN
Retrocopy DKLKSLQKDEV*QFMSFKESTXXXC>ASCLSQNDCKLDTATNNIFQNPELYIQESIKGSLNGKMFEQLYN

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMAELGCDSIDKLKAQ
          RYK.PQ.ENK...DGIQ.FCDDL........VL.....F..AT.CE.SKQEF.D....LG..S..KLKAQ
Retrocopy RYKHPQAENKTRMDGIQ*FCDDLDSTKPAL-VLGSLHEFQRATLCESSKQEFVDSVTDLG*ASREKLKAQ

Parental  IPKMEQELKEPGRFKDFY
          IPKM..E..E...FKD..
Retrocopy IPKMQPEF*EQE*FKDVF

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	10.01 RPM
SRP017611_kidney	0.00 RPM	9.42 RPM
SRP017611_liver	0.00 RPM	15.45 RPM
SRP040447_lung	0.00 RPM	12.56 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.73 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_870 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_870 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 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232, retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Cavia porcellus	ENSCPOG00000008945	2 retrocopies	retro_cpor_1176, retro_cpor_1179,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870 ,
Dasypus novemcinctus	ENSDNOG00000019073	2 retrocopies	retro_dnov_1494, retro_dnov_840,
Echinops telfairi	ENSETEG00000000166	1 retrocopy	retro_etel_1460,
Homo sapiens	ENSG00000043093	1 retrocopy	retro_hsap_3502,
Gorilla gorilla	ENSGGOG00000010767	1 retrocopy	retro_ggor_2368,
Macaca mulatta	ENSMMUG00000010552	1 retrocopy	retro_mmul_1782,
Mustela putorius furo	ENSMPUG00000002369	1 retrocopy	retro_mputfur_919,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009,
Nomascus leucogenys	ENSNLEG00000005983	1 retrocopy	retro_nleu_793,
Otolemur garnettii	ENSOGAG00000000658	1 retrocopy	retro_ogar_3499,
Pan troglodytes	ENSPTRG00000015661	1 retrocopy	retro_ptro_2374,
Tarsius syrichta	ENSTSYG00000012276	1 retrocopy	retro_tsyr_669,