RetrogeneDB ID: retro_cpor_1081

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_44:14049691..14050110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB14
• Ensembl ID: ENSCPOG00000006688
• Aliases: None
• Description: None

Sequence

>retro_cpor_1081
AAGGAATGATTCAGAGCTGTTCCAGGAAACTCCTGCAGAGGGGCTGCAGGCACATGTGTGATGTGGGATGCCACTAGGAC
ACATGGCCTTGGAAGCAGCTGGGTGACAGATGTGAGGAATCCCACCAGTCCAAAAACAGTAACAGTTCTAGAAAGTAAGC
AGCTTCCAAGACACAGAGAGATTTTACATGTGGAGAAGTCATGCAGTTCCTGAAGATAATGGCTTTCTGCTCCTTGCAGC
AGATAGAAGAATGGGAGAGAATGCAGAGGATGCTTTCCTGGAGCCTGCCAAGAAGATCCCTCAGAATGTGCAGGTTGGAA
GCCTGCTCTAACTGATGCTGAGTCTGGGTACAACACAGACCCTCAGCCCCACAAAGGGGGAGCTGAGAAATGAGCTCCAA
ACCCAGAGCAGGCTGTGGC

Alignment

ORF - retro_cpor_1081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.68 %
• Parental protein coverage: 67.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNK-ADLEAQRDVTYEE
          .E.FRAV.....RGAAG.....D.TR..T....SSW.TD.RN.T.P.T.......K.A....QRD.T..E
Retrocopy KE*FRAVPGNSCRGAAGTCVMWDATR--THGLGSSWVTDVRNPTSPKT-VTVLESK<AASKTQRDFTCGE

Parental  AKQFA-EENGLLFLEASAKTGENVEDAFLEAAKKIYQNIQDGSL-DLNAAESG-VQHKPSAPQGGRLTSE
          ..QF..E.NG.L.L.A....GEN.EDAFLE.AKKI.QN.Q.GSL..L..AESG.VQH.PSAPQ.G.....
Retrocopy VMQFL<EDNGFLLLAADRRMGENAEDAFLEPAKKIPQNVQVGSL<ALTDAESG<VQHRPSAPQRGS*EMS

Parental  PQPQREGCG
          ..P.R.GCG
Retrocopy SKP-RAGCG

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	54.24 RPM
SRP017611_kidney	0.00 RPM	41.25 RPM
SRP017611_liver	0.00 RPM	55.63 RPM
SRP040447_lung	0.00 RPM	38.97 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.42 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1081 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1081 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003669	1 retrocopy	retro_chof_2175,
Cavia porcellus	ENSCPOG00000006688	1 retrocopy	retro_cpor_1081 ,
Cavia porcellus	ENSCPOG00000026575	1 retrocopy	retro_cpor_839,
Myotis lucifugus	ENSMLUG00000009818	1 retrocopy	retro_mluc_1875,
Oryctolagus cuniculus	ENSOCUG00000013654	1 retrocopy	retro_ocun_1667,
Otolemur garnettii	ENSOGAG00000012973	1 retrocopy	retro_ogar_710,
Pelodiscus sinensis	ENSPSIG00000003919	1 retrocopy	retro_psin_66,
Sarcophilus harrisii	ENSSHAG00000017800	1 retrocopy	retro_shar_80,