RetrogeneDB ID: retro_cpor_839

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:70355938..70356395(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2B
• Ensembl ID: ENSCPOG00000026575
• Aliases: None
• Description: None

Sequence

>retro_cpor_839
GCCAGGCAAGAATCCTTCCATTCTATCACCCATTCCTTTTACAAGGGAGCAGCAAGAGCACTCCTAGTGTATAACATTAC
AAGGCTGAAATGTTCAGCCACATGACCTCATAGCTAACGGGTGCCTGCTAGCATTCTAGATCCACCATGGTTATCAGGCT
GGTTGGGAATAAGGGTGATTTAGGGTCCCACAGAGATGTGAAGAGAGAGGAAGGATAAGCTTTGCTCAGGAGCATGGATT
GATATTCATAGAAACTTCAGTCAAAATTGCCTGAAATGTTGAAGAGGCCTTATTAACACAGCCAAAGAAATCTATAAGAA
AATCCAGCAGGGTTTATTTGATGTCCACAATGAGGCAAGTGCCAGCAAGACTGAGCTCAGCAGTCAATTTCAACAACAGC
CAGATGTGGTGCCTGCCAGGGAACTCTGGAGATACAGAGTCTGACTCTGGCTGCTGC

Alignment

ORF - retro_cpor_839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.18 %
• Parental protein coverage: 71.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AGQESFRSITRSYYRGAAGALLVYDITR-RETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKR
          A.QESF.SIT.S.Y.GAA.ALLVY.ITR..E.F.H.TS.L..A..HS.S.MVI.L.GNK.DL.S.RDVKR
Retrocopy ARQESFHSITHSFYKGAARALLVYNITR<AEMFSHMTS*LTGAC*HSRSTMVIRLVGNKGDLGSHRDVKR

Parental  EEGEA-FAREHGLIFMETSAKTACNVEEA-FINTAKEIYRKIQQGLFDVHNEANGIKIG-PQQSIATSAG
          EEG.A.FA.EHGLIF.ETS.K.A.NVEEA..INTAKEIY.KIQQGLFDVHNEA...K....QQSI.T.A.
Retrocopy EEG*A<FAQEHGLIFIETSVKIA*NVEEA<LINTAKEIYKKIQQGLFDVHNEASASKTE<AQQSISTTAR

Parental  PGAC-PRNSRDTGSDSGCC
          .GAC.P.NS.DT.SDSGCC
Retrocopy CGAC<PGNSGDTESDSGCC

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	17.31 RPM
SRP017611_kidney	0.00 RPM	4.61 RPM
SRP017611_liver	0.00 RPM	5.05 RPM
SRP040447_lung	0.00 RPM	15.01 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_839 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_839 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000044207	1 retrocopy	retro_btau_991,
Canis familiaris	ENSCAFG00000005641	1 retrocopy	retro_cfam_1510,
Choloepus hoffmanni	ENSCHOG00000000710	3 retrocopies	retro_chof_2314, retro_chof_706, retro_chof_900,
Cavia porcellus	ENSCPOG00000006688	1 retrocopy	retro_cpor_1081,
Cavia porcellus	ENSCPOG00000026575	1 retrocopy	retro_cpor_839 ,
Macropus eugenii	ENSMEUG00000010489	2 retrocopies	retro_meug_2160, retro_meug_91,
Myotis lucifugus	ENSMLUG00000001902	3 retrocopies	retro_mluc_1243, retro_mluc_1251, retro_mluc_2103,
Sorex araneus	ENSSARG00000004969	1 retrocopy	retro_sara_97,
Ictidomys tridecemlineatus	ENSSTOG00000001886	1 retrocopy	retro_itri_468,