RetrogeneDB ID: retro_cpor_957

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_37:8053155..8053818(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PITPNB
• Ensembl ID: ENSCPOG00000012298
• Aliases: None
• Description: None

Sequence

>retro_cpor_957
AAGGATGGAGAGAAGGGCCAGTACACACACAAGATCTACCACTTGCAGAACAAAGTACCCACATTTGTCTGAATGCTGGC
CCCAGAGGGAGCCCTAAATATACCCGAGAAGGCATGGAATGCCTACCCTTACTGCAGAACGGTTATTACAAATGAGTACA
TGAAGGAAGACTTTCTGATTAAAATTGAGACCTGGCACAAACCGGATCTTGGCACCCAGGAGAATGTGCATAAGCTGGAG
CCTGAGACATGGAAACATGTGGAAGCCATATATACAGACATTGCAGATCAAAGCCAAGTACTTAGCAAGGATTGCAAGGC
AGAAGAAGACCCAGCAAAATTTAAATCTGTCAAAATAGGCCGAGGACCTTTGGGGACAAATTGGAAGCAAGAACTTGTAA
ATCAGAAAGTCTGCCCATATATGTGTGCGTACAAACTGGTTAGTGTCAAGTTCAAGTGGTGGGGCCTGCAGAGTAAAGTG
GAGAACTTTATACACAAGCAAGAGAGGCGTCTGTTTACAAATTTCCACAGGCAGCTGTTCTGTTGGCTGGACAAGTGGGT
TGATCTGACTATGGACGGCATTCGAAGGATGGAAGAAGAGACGAAGAGACAGCTGGATGAGATGAGACAAAAAGACCCAG
TGAAAGGAATGACAGCAGATGAC

Alignment

ORF - retro_cpor_957 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.04 %
• Parental protein coverage: 81.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDGEKGQFTHKIYHLKSKVPTFVRMIAPEGSLVFHEKAWNSYPYCRTIVTNEYMKDDFFIKIETWHKPDL
          KDGEKGQ.THKIYHL..KVPTFV.M.APEG.L...EKAWN.YPYCRT..TNEYMK.DF.IKIETWHKPDL
Retrocopy KDGEKGQYTHKIYHLQNKVPTFV*MLAPEGALNIPEKAWNAYPYCRTVITNEYMKEDFLIKIETWHKPDL

Parental  GTLENVHDLDPNTWKTVEVVHIDIADRSQVEPGDYKANEDPALYQSVKTKRGPLGPNWKKELANNPDCPQ
          GT.ENVH.L.P.TWK.VE....DIAD.SQV...D.KA.EDPA...SVK..RGPLG.NWK.EL.N...CP.
Retrocopy GTQENVHKLEPETWKHVEAIYTDIADQSQVLSKDCKAEEDPAKFKSVKIGRGPLGTNWKQELVNQKVCPY

Parental  MCAYKLVTIKFKWWGLQNKVENFIQKQEKRIFTNFHRQLFCWIDKWIDLTMEDIRRMEDETQKELETMRK
          MCAYKLV..KFKWWGLQ.KVENFI.KQE.R.FTNFHRQLFCW.DKW.DLTM..IRRME.ET...L..MR.
Retrocopy MCAYKLVSVKFKWWGLQSKVENFIHKQERRLFTNFHRQLFCWLDKWVDLTMDGIRRMEEETKRQLDEMRQ

Parental  KGSVRGTSAAD
          K..V.G..A.D
Retrocopy KDPVKGMTADD

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	21.11 RPM	25.59 RPM
SRP017611_kidney	7.43 RPM	17.90 RPM
SRP017611_liver	6.14 RPM	22.46 RPM
SRP040447_lung	8.73 RPM	17.63 RPM
SRP040447_skeletal_muscle	4.59 RPM	5.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_957 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_957 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012309	2 retrocopies	retro_chof_2374, retro_chof_860,
Cavia porcellus	ENSCPOG00000012298	1 retrocopy	retro_cpor_957 ,
Macropus eugenii	ENSMEUG00000010442	3 retrocopies	retro_meug_392, retro_meug_689, retro_meug_786,
Oryctolagus cuniculus	ENSOCUG00000000511	1 retrocopy	retro_ocun_1620,
Otolemur garnettii	ENSOGAG00000000391	1 retrocopy	retro_ogar_1300,
Ochotona princeps	ENSOPRG00000002540	1 retrocopy	retro_opri_931,
Tupaia belangeri	ENSTBEG00000000293	1 retrocopy	retro_tbel_4285,
Takifugu rubripes	ENSTRUG00000018546	1 retrocopy	retro_trub_36,
Tarsius syrichta	ENSTSYG00000001148	1 retrocopy	retro_tsyr_503,
Tursiops truncatus	ENSTTRG00000001278	2 retrocopies	retro_ttru_1060, retro_ttru_1439,