RetrogeneDB ID: retro_cpor_586

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:49764069..49764599(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSCPOG00000011463
• Aliases: None
• Description: None

Sequence

>retro_cpor_586
TTATCACGTGCAATTGAAAGGAAGCAGAATTTTCTGAGGCTAAATAGAAGACTCTAGCAAAGTAGTGCTTGGCAATTCAG
GATGACAGTACCAAGGGAGAATCCAGCAGAATTATAGGTTTGGTAACACTAAGCTAAGCCGAAGAGGAAGAGTAACGCCT
GGAAGAGCCGTCCTCATGGAGGGATCACTGGCCTGCAGCCGGGAAGGCACCTGGGATTCGGAAAGGAGTTAGCACTATGA
ATTGTCCACCTCTAAGTGGCAAGAGTGTAGAATGATATTTTCTTGTGTTAAGAAGGAAAACAAACCTTCTGACACAAAAT
GAAGTGCAAAGAAAACCCCTGCAGTTCTCAAGAGACCCTAACCAGTTAAACAGAAAGAATAAAATCCCAGCTAATTTTAC
CAGGAGTAGAAATAAATTGAGTCATCAGAAAGACACCTGTCAGCCAACTTCTCTTTTCTGAAGAGGCCAGACGGTTCAGG
CCCAGTTGAACACAGAACAAGCGCTAGATGATGTAGTAGCAAAGAGAACT

Alignment

ORF - retro_cpor_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 55.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNRKEGKKHNFPRLNRRLQQSSARQFRMRV-RWGIQQNSGFGKTSLSRRGKVMPG-KRRPYGVITGL-AA
          L.R....K.NF.RLNRRL.QSSA.QFRM.V....IQQN..FG.T.LSRRG.V.PG.K.RP.G.ITGL.AA
Retrocopy LSRAIERKQNFLRLNRRL*QSSAWQFRMTV>QGRIQQNYRFGNTKLSRRGRVTPG<KSRPHGGITGL<AA

Parental  RKATGIRKGVSPMNRPPLSDKNIERYFPVLKRKANLLRQNDVQRKPATVLKRPNQLNRKSNIPANFTRSA
          .KA.GIRKGVS.MN.PPLS.K..E.YF.VL.RK.NLL.QN.VQRKP......PNQLNRK..IPANFTRS.
Retrocopy GKAPGIRKGVSTMNCPPLSGKSVE*YFLVLRRKTNLLTQNEVQRKPLQFSRDPNQLNRKNKIPANFTRSR

Parental  NKLSHQKDTRQATFLFRRGLKVQAQLNTEQLLDDVVAKRT
          NKLSHQKDT.Q.T.LF.RG..VQAQLNTEQ.LDDVVAKRT
Retrocopy NKLSHQKDTCQPTSLF*RGQTVQAQLNTEQALDDVVAKRT

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	14.67 RPM
SRP017611_kidney	0.00 RPM	14.03 RPM
SRP017611_liver	0.00 RPM	8.84 RPM
SRP040447_lung	0.00 RPM	12.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.99 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_586 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_586 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.

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586 ,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,