RetrogeneDB ID: retro_cpor_330

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_128:3264070..3264716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM248
• Ensembl ID: ENSCPOG00000000830
• Aliases: None
• Description: None

Sequence

>retro_cpor_330
GAGAATCAGGAAATAAAATAGTGCCACATCTTTCAAAGGACAGCACAACTTCAGAGAGCAGTGACCAGTGGGGCGGCCAA
AGTGCCCACCCAATCCCCCCAGTCCCTGGAGGACTCAGGCTGGGCTAACATCTCAATTGCAGTCACCCTCACCCTGGATC
CCCTCAAGCCATTCAGAGGCTTCTCCCGTGGTGGTACCCATCTGTACTGGACCATTTCGGGACATCAGATTGTTCTTTCG
GGTGGAGAAGCCCAGGAGGAGATAGGAAGTAAACATTACCTTTCCCTTGCCCGTGGCTTGGAGCTTGGACATCTGTGTTC
TTCGTGGCCACTGTGAGCAGGTGATGTCCACATCCTGCATGATCCTCATGTCCATGTCCAATATCTTCCCTGTTACTGTG
CAGCCTCCACACAGTGTCCCCGAAAGGCACTGCAATGCCACACTCTGGCACACGATCTTCACAGCTCCCGGCGATGCCAA
TACAAAATATGTGCAAGACTACAAACCTTGCTGGTGCTACTGTGGGGGCATTGGCAAAGACCGTTGTGCTTTAAGTCCCA
GACTTACAGCTATTGTTCCAGATGATGACATTTCATTAATAAATCCACAGCTCATGCATACCACTTACTTCCGCTTTGTG
GTGGTA

Alignment

ORF - retro_cpor_330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.04 %
• Parental protein coverage: 67.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ENETLK--HLSNDSTASESTVTSGQARVSTQSPQALEDSGPVNISVAITLTLDPLKPFGGFSRNVTHLYS
          EN...K..H...........VTSG.A.V.TQSPQ.LEDSG..NIS.A.TLTLDPLKPF.GFSR..THLY.
Retrocopy ENQEIK*CHIFQRTAQLQRAVTSGAAKVPTQSPQSLEDSGWANISIAVTLTLDPLKPFRGFSRGGTHLYW

Parental  TILGHQIGLSGREAHEEI-NITFTLP--TAWSSDDCALHGHCEQVVFTTCMTLTASPDVFPVTVQPPHCV
          TI.GHQI.LSG.EA.EEI.....T.P...AWS.D.C.L.GHCEQV..T.CM.L......FPVTVQPPH.V
Retrocopy TISGHQIVLSGGEAQEEI>EVNITFPLPVAWSLDICVLRGHCEQVMSTSCMILMSMSNIFPVTVQPPHSV

Parental  PDTYSNATLWYKIFTTARDANTKYAQDYNPFWCYKGAIGKVYHALNPKLTVIVPDDDRSLINLHLMHTSY
          P....NATLW..IFT...DANTKY.QDY.P.WCY.G.IGK...AL.P.LT.IVPDDD.SLIN..LMHT.Y
Retrocopy PERHCNATLWHTIFTAPGDANTKYVQDYKPCWCYCGGIGKDRCALSPRLTAIVPDDDISLINPQLMHTTY

Parental  FLFVMV
          F.FV.V
Retrocopy FRFVVV

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	22.55 RPM
SRP017611_kidney	0.00 RPM	40.83 RPM
SRP017611_liver	0.04 RPM	24.64 RPM
SRP040447_lung	0.00 RPM	49.13 RPM
SRP040447_skeletal_muscle	0.01 RPM	31.07 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_330 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_330 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004278	1 retrocopy	retro_cjac_2145,
Cavia porcellus	ENSCPOG00000000830	1 retrocopy	retro_cpor_330 ,
Echinops telfairi	ENSETEG00000015971	1 retrocopy	retro_etel_2097,
Homo sapiens	ENSG00000106609	1 retrocopy	retro_hsap_3093,
Gorilla gorilla	ENSGGOG00000022776	1 retrocopy	retro_ggor_2124,
Myotis lucifugus	ENSMLUG00000000616	1 retrocopy	retro_mluc_1974,
Macaca mulatta	ENSMMUG00000015843	1 retrocopy	retro_mmul_1973,
Nomascus leucogenys	ENSNLEG00000013326	1 retrocopy	retro_nleu_2235,
Pan troglodytes	ENSPTRG00000019253	1 retrocopy	retro_ptro_2089,
Pteropus vampyrus	ENSPVAG00000002978	2 retrocopies	retro_pvam_988, retro_pvam_997,
Sorex araneus	ENSSARG00000001884	1 retrocopy	retro_sara_563,