RetrogeneDB ID: retro_cpor_103

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:27610633..27611509(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000012916
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OTUD6B
• Ensembl ID: ENSCPOG00000013595
• Aliases: None
• Description: None

Sequence

>retro_cpor_103
ATGGAAGATCTCCAGAGAGAACGTCAGCGGATGATGCGTCGCCATTGCCGTGAAAAGGAAGAACTAGAGGCCCAAATCCA
AAGCATGAAGCGCTCCGTCCCCAAGAGCGACAAAAAGCAAAGAAAGCAATTGCGCCTCGACACGACTCGCCTCCAGGCTG
AGATGGAACAGAGGCATCAGCAGGAGTTAGAGAAGTTCCAAGAGAACTTCCCTGGTAACGGCACTCTGGATTCTATCACC
GAAAATCTGGCTAAGATGAATCTCGAGAACCAGCACCCCCACACCTCTAGGGCACAGAAAAGGCGAGAAAGAAAGGAGGC
CCTGGAGAGAGAAGAACAGGAAAGGATCCTTGTGGCTGAGATGGAGCATCTGGCCAGCTTCCGCCTAGAGGAGGAGAAAA
AGCTCGCAACCATCTTGGGTGCCAAGTATCTGGAAATGAAGGAAATCCCTGCTGACAGCCACTGCATGTACCGCGCCATC
CAAGACCAGCTGGTGTTCTCCGTGACGGTTGAGAGCTTGCGCCGCCGCACAGCTGACTACTTGCGGAAGCACGTCGATGA
CTTTCTGCCCTTCTTCAGCGACCCTGAAACGGGTGACGCCTATGATCCTACGGACTTTATGGCCCACTGCGACAACATCG
TTTCCCGCGGATCGTGGGGTGGCCAGCTGGAGCTGAGGGCCCTGTCGCACGTCCTGCAGACCCCCATCGAAGTGGTCCAG
GCCAATTCACCTTCCTTGCTCGTCGGGGAGGAATACCACAAGAAGCCGCTCACCCTAGTCTACGTGCACTACGCCCGCAG
CCTCGGGGAGCACTACAATTCCGTGAAGCCACTCGAGGCCAGTGCGGCGAGCAGCGCCGCCCCGCGCCTCTTCTAG

Alignment

ORF - retro_cpor_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.9 %
• Parental protein coverage: 52.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEQLVRRHRKEKKELQAKIQGMKNAVPKNDKRRRKQLTEDVAKLEKEMEQKHREELEQLKLAAKEN-KI
          E.....RRH..EK.EL.A.IQ.MK..VPK.DK..RKQL..D...L..EMEQ.H..ELE........N...
Retrocopy ERQRMMRRHCREKEELEAQIQSMKRSVPKSDKKQRKQLRLDTTRLQAEMEQRHQQELEKFQENFPGNGTL

Parental  DSVAVNIANLVLENQPPRISKAQKRRNLNAALEKEREERIAEAEIENLSGARHIENEKLAQILAARELEI
          DS...N.A...LENQ.P..S.AQKRR....ALE.E..ERI..AE.E.L...R..E..KLA.IL.A..LE.
Retrocopy DSITENLAKMNLENQHPHTSRAQKRRERKEALEREEQERILVAEMEHLASFRLEEEKKLATILGAKYLEM

Parental  KQIPSDGHCMYKAIEDQL
          K.IP.D.HCMY.AI.DQL
Retrocopy KEIPADSHCMYRAIQDQL

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	11.33 RPM
SRP017611_kidney	0.00 RPM	9.42 RPM
SRP017611_liver	0.00 RPM	7.36 RPM
SRP040447_lung	0.00 RPM	3.78 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.43 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_103 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_103 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 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006971	1 retrocopy	retro_amel_74,
Bos taurus	ENSBTAG00000003481	2 retrocopies	retro_btau_236, retro_btau_969,
Choloepus hoffmanni	ENSCHOG00000004266	2 retrocopies	retro_chof_1969, retro_chof_2069,
Cavia porcellus	ENSCPOG00000013595	1 retrocopy	retro_cpor_103 ,
Equus caballus	ENSECAG00000018205	1 retrocopy	retro_ecab_44,
Felis catus	ENSFCAG00000029900	1 retrocopy	retro_fcat_124,
Loxodonta africana	ENSLAFG00000011002	1 retrocopy	retro_lafr_16,
Microcebus murinus	ENSMICG00000012278	1 retrocopy	retro_mmur_1222,
Myotis lucifugus	ENSMLUG00000016954	1 retrocopy	retro_mluc_1226,
Macaca mulatta	ENSMMUG00000013396	1 retrocopy	retro_mmul_350,
Monodelphis domestica	ENSMODG00000007551	2 retrocopies	retro_mdom_119, retro_mdom_1326,
Mustela putorius furo	ENSMPUG00000009194	1 retrocopy	retro_mputfur_51,
Mus musculus	ENSMUSG00000040550	1 retrocopy	retro_mmus_2456,
Nomascus leucogenys	ENSNLEG00000002420	1 retrocopy	retro_nleu_2365,
Oryctolagus cuniculus	ENSOCUG00000000218	1 retrocopy	retro_ocun_29,
Otolemur garnettii	ENSOGAG00000011298	1 retrocopy	retro_ogar_228,
Ochotona princeps	ENSOPRG00000007655	1 retrocopy	retro_opri_413,
Pan troglodytes	ENSPTRG00000020413	1 retrocopy	retro_ptro_3120,
Sus scrofa	ENSSSCG00000006120	1 retrocopy	retro_sscr_52,
Ictidomys tridecemlineatus	ENSSTOG00000002954	1 retrocopy	retro_itri_9,
Tupaia belangeri	ENSTBEG00000017070	1 retrocopy	retro_tbel_304,
Tursiops truncatus	ENSTTRG00000004345	1 retrocopy	retro_ttru_1207,