RetrogeneDB ID: retro_cpor_470

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:28402992..28403657(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADIPOR1
• Ensembl ID: ENSCPOG00000000482
• Aliases: None
• Description: None

Sequence

>retro_cpor_470
TTATCTTCCCACAAAGGATCTGTGGTAACACGTGCAATAGGACTCCTGCCAGTAACAGGGAAACTGACACGGTTGATCTG
CCTCAACTGGGACCTCCGCTAGAAGAGAAGGGGAAGCAGGTAATTGCCAAGCCAACGGAAGCCGAAGATGAGCAAACATG
CCCTGTTCCCCAGGAAGAGGACAAGGAGGTGCGGGTGCTGATGTTTCCTCTGCAAGCCCAGCATGCCATGGAGAAGATGG
AGGAGTTTGTGTACAAGTTCTGGGAGGGACGCTGGAGTGTCTTCCCATATGATGTGCTCCCCAACTGGCTGAAGGACAAT
GATTACCTATTATATGGCTACAGATTACTCATTCCCTCTTCTCAGGCTTGCTTCCAGATCATCTTCTGCATTCACACATA
AACTGGCAACATCTGGACCAATCTGCTTTGTTTTGTGCTCTTTCTCTTTTTGGGAATCCTGATCATGCCCCGACCAAATA
TGTTCTTCATGACACTGCTGCAGGAGAAGGTGGTTTGGGGGATGTTCTTTTGGGTGCTCTGCCTCAGCTTCTCATGGCTC
TTTCACACTGTCTATTGTCATTCAGAGAAAGTCTCACAGACTTTTTCCAAATTAGACTCTTCAGAAATTGCTCTACTGAT
TATGGGGAGCTTTATCCCCTGGCTC

Alignment

ORF - retro_cpor_470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 59.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSHKGSVVAQG-NGTPASNRETDTMELAELGPLLEEKGKRVIANPTKAEDEQTCPVPQEEEEEVRVLTL
          .SSHKGSVV....N.TPASNRETDT..L..LGP.LEEKGK.VIA.PT.AEDEQTCPVPQEE..EVRVL..
Retrocopy LSSHKGSVVTRA<NRTPASNRETDTVDLPQLGPPLEEKGKQVIAKPTEAEDEQTCPVPQEEDKEVRVLMF

Parental  PLQAHHAMEKMEEFVYKVWEGRWRVIPYDVLPDWLKDNDYLLHGHRPPMPSFRACFKSIFRIHTETGNIW
          PLQA.HAMEKMEEFVYK.WEGRW.V.PYDVLP.WLKDNDYLL.G.R...PS..ACF..IF.IHT.TGNIW
Retrocopy PLQAQHAMEKMEEFVYKFWEGRWSVFPYDVLPNWLKDNDYLLYGYRLLIPSSQACFQIIFCIHT*TGNIW

Parental  THLLGFVLFLFLGILTMLRPNMYFMAPLQEKVVFGMFFLGAVLCLSFSWLFHTVYCHSEKVSRTFSKLDY
          T.LL.FVLFLFLGIL.M.RPNM.FM..LQEKVV.GMFF...VLCLSFSWLFHTVYCHSEKVS.TFSKLD.
Retrocopy TNLLCFVLFLFLGILIMPRPNMFFMTLLQEKVVWGMFFW--VLCLSFSWLFHTVYCHSEKVSQTFSKLDS

Parental  SGIALLIMGSFVPWL
          S.IALLIMGSF.PWL
Retrocopy SEIALLIMGSFIPWL

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	51.25 RPM
SRP017611_kidney	0.00 RPM	70.56 RPM
SRP017611_liver	0.00 RPM	43.40 RPM
SRP040447_lung	0.00 RPM	70.82 RPM
SRP040447_skeletal_muscle	0.00 RPM	163.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_470 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_470 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 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012199	1 retrocopy	retro_amel_1853,
Choloepus hoffmanni	ENSCHOG00000006450	8 retrocopies	retro_chof_1127, retro_chof_1222, retro_chof_1917, retro_chof_2218, retro_chof_2380, retro_chof_471, retro_chof_749, retro_chof_995,
Callithrix jacchus	ENSCJAG00000006268	3 retrocopies	retro_cjac_2262, retro_cjac_740, retro_cjac_741,
Cavia porcellus	ENSCPOG00000000482	1 retrocopy	retro_cpor_470 ,
Dipodomys ordii	ENSDORG00000006876	1 retrocopy	retro_dord_19,
Felis catus	ENSFCAG00000013565	1 retrocopy	retro_fcat_1514,
Loxodonta africana	ENSLAFG00000003520	1 retrocopy	retro_lafr_277,
Macropus eugenii	ENSMEUG00000015439	1 retrocopy	retro_meug_516,
Microcebus murinus	ENSMICG00000007942	3 retrocopies	retro_mmur_1199, retro_mmur_184, retro_mmur_764,
Myotis lucifugus	ENSMLUG00000016102	2 retrocopies	retro_mluc_1275, retro_mluc_200,
Macaca mulatta	ENSMMUG00000007046	1 retrocopy	retro_mmul_1322,
Mustela putorius furo	ENSMPUG00000011215	1 retrocopy	retro_mputfur_550,
Otolemur garnettii	ENSOGAG00000033821	4 retrocopies	retro_ogar_1558, retro_ogar_1624, retro_ogar_2838, retro_ogar_783,
Ochotona princeps	ENSOPRG00000004528	3 retrocopies	retro_opri_101, retro_opri_1050, retro_opri_392,
Pongo abelii	ENSPPYG00000000342	1 retrocopy	retro_pabe_1072,
Sorex araneus	ENSSARG00000007680	1 retrocopy	retro_sara_25,
Ictidomys tridecemlineatus	ENSSTOG00000015459	3 retrocopies	retro_itri_215, retro_itri_257, retro_itri_512,
Tupaia belangeri	ENSTBEG00000015149	2 retrocopies	retro_tbel_1501, retro_tbel_1804,
Tarsius syrichta	ENSTSYG00000001491	1 retrocopy	retro_tsyr_125,
Tursiops truncatus	ENSTTRG00000006381	2 retrocopies	retro_ttru_1055, retro_ttru_863,