RetrogeneDB ID: retro_cpor_1289

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_65:3125067..3125839(-)
• Located in intron of: ENSCPOG00000011275

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_1289
AACAAGTTGAAATCATTGCAGAAAGATAAAGTTCGACAGTTTATTATCATCACACAATCCAGTGAAAAAAATCTTTCTCA
AAGTTGTCTTTCTCAAAATGACTGAAAGTTAAATGTTGCAACAGATGTTTTCCAAAATCCTGAACTTTACATACGAGAGA
ATGCAAAAGGATCATTAGACAGGAAGAAGTTAGAACAACTGTACATTAGGTACAAAGAGCCTCAACATGAAAACAAAATT
GGAATAGATGGTATACAGCAATTTGGTGATGACCTGGCACTTGATCCAGCTAGCATCAGTGTTCTGATCATTGCATGGAA
GTTCAGAGCAGCAACAACACAATGTGAGTTCTCCAAGCAGTTGTTCATGGATGGCATGAGAGAATTAGGATGTGATAGCA
TAGAAAAGCTAACGGCTCAGATACTCAAGATGGAACAAGAACTGAAAGAACCAGGATGATTTAAGGATTTTTACCAGTTT
ACTTTTAATTTTGCAAAGAATTCAAGACCAAAAGGATTAGATCCAGTAGCCATTGTCTACTGGAGCTTAGTGCTTATTGG
AAGATTTAAATTCTTAGACTTATGAAGTTATCTTTTTGTCAGGATTTCATAAACAATCAATACCAAAAGATACTTGGAAT
CTTCTTTTAGACTTCCCTACAATAGCTGAAGATGAAATGTCTACCTATGATGAAGGATCATGGCCTGTTCTCATTGATGA
CTTTGTGGAATTTCCATGCCCTCCCATTGCTAGAACAAAAAATACAACAGTC

Alignment

ORF - retro_cpor_1289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSEKT-AVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYN
          NKLKS.QKDKVRQF.I.TQSSEK....SCLSQND.KL.VATD..FQNPELYIRE..KGSLDRKKLEQLY.
Retrocopy NKLKSLQKDKVRQFIIITQSSEKNLSQSCLSQND*KLNVATD-VFQNPELYIRENAKGSLDRKKLEQLYI

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAAT-QCEFSKQEFMDGMAELGCDSIDKLKA
          RYK.PQ.ENKIGIDGIQQF.DDLALDPASISVLIIAWKFRAAT.QCEFSKQ.FMDGM.ELGCDSI.KL.A
Retrocopy RYKEPQHENKIGIDGIQQFGDDLALDPASISVLIIAWKFRAATTQCEFSKQLFMDGMRELGCDSIEKLTA

Parental  QIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNK-FLLEHHKRSI
          QI.KMEQELKEPG.FKDFYQFTFNFAKN...KGLD...AI.YW.LVL.GRFKFLDL....FL...HK.SI
Retrocopy QILKMEQELKEPG*FKDFYQFTFNFAKNSRPKGLD-PVAIVYWSLVLIGRFKFLDL*SY>FLSGFHKQSI

Parental  PKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTAV
          PKDTWNLLLDF.T...D.MS.YD.EG.WPVLIDDFVEF..P.IA.TK.T.V
Retrocopy PKDTWNLLLDFPTIAEDEMSTYD-EGSWPVLIDDFVEFPCPPIARTKNTTV

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	0.29 RPM	10.01 RPM
SRP017611_kidney	1.05 RPM	9.42 RPM
SRP017611_liver	0.57 RPM	15.45 RPM
SRP040447_lung	0.83 RPM	12.56 RPM
SRP040447_skeletal_muscle	0.12 RPM	8.73 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1289 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1289 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.

---

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,