RetrogeneDB ID: retro_cpor_126

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_32:9359663..9360011(-)
• Located in intron of: ENSCPOG00000005504

Retrocopy information

• Ensembl ID: ENSCPOG00000000100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DNAJC19
• Ensembl ID: ENSCPOG00000021198
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 19 [Source:HGNC Symbol;Acc:30528]

Sequence

>retro_cpor_126
ATGGCCCGTACAGTGGTAGCAGTTGGACTGACCATTGCTGCTGCAGGATTTGCAGGCCGTTACATTTTACAAGCCATGAA
GCATATGGAACCGCAAGTAAAACACGTTTTTCAGAGTCTACCAAAATCTGCCTTCAGTGGTGGCTATTACAGAGGTGGAC
TTAAACCCAAAATGACAAAATGGGAAGCAGAATTAATACTAGGTGTCAGCCCTACTGCCAGTAAAGAAAAAATAAGTGAT
GCTCATCGACGAATTGTGCTCTTAAATCATCCAGACAAAGGAGGATCTCCTTACATGGCAGCCAAAATCAATGAAGCTAA
AGATTTACTAGGTCAAGCTAAAAAATGA

Alignment

ORF - retro_cpor_126 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 72.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASTVIAVGLTIAAAGFAGRYVLQAMKHMEPQVKQVFQSLPKSAFSGGYYRGGFEPKMTKREAALILGVSP
          A.TV.AVGLTIAAAGFAGRY.LQAMKHMEPQVK.VFQSLPKSAFSGGYYRGG..PKMTK.EA.LILGVSP
Retrocopy ARTVVAVGLTIAAAGFAGRYILQAMKHMEPQVKHVFQSLPKSAFSGGYYRGGLKPKMTKWEAELILGVSP

Parental  TANKGKIRDAHRRIMLLNHPDKG
          TA.K.KI.DAHRRI.LLNHPDKG
Retrocopy TASKEKISDAHRRIVLLNHPDKG

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	6.56 RPM
SRP017611_kidney	0.00 RPM	11.72 RPM
SRP017611_liver	0.04 RPM	10.88 RPM
SRP040447_lung	0.00 RPM	6.08 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.75 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_126 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_126 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 29 parental genes, and 136 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012255	6 retrocopies	retro_amel_1087, retro_amel_155, retro_amel_252, retro_amel_283, retro_amel_744, retro_amel_994,
Bos taurus	ENSBTAG00000023513	1 retrocopy	retro_btau_127,
Callithrix jacchus	ENSCJAG00000012795	10 retrocopies	retro_cjac_1008, retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890, retro_cjac_3060, retro_cjac_914,
Cavia porcellus	ENSCPOG00000003485	1 retrocopy	retro_cpor_327,
Cavia porcellus	ENSCPOG00000021198	1 retrocopy	retro_cpor_126 ,
Dasypus novemcinctus	ENSDNOG00000019067	1 retrocopy	retro_dnov_49,
Erinaceus europaeus	ENSEEUG00000006955	9 retrocopies	retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi	ENSETEG00000006897	7 retrocopies	retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis	ENSFALG00000008296	1 retrocopy	retro_falb_28,
Felis catus	ENSFCAG00000010591	7 retrocopies	retro_fcat_1250, retro_fcat_1481, retro_fcat_1603, retro_fcat_1837, retro_fcat_475, retro_fcat_511, retro_fcat_982,
Gallus gallus	ENSGALG00000008852	1 retrocopy	retro_ggal_17,
Gorilla gorilla	ENSGGOG00000009120	7 retrocopies	retro_ggor_1037, retro_ggor_1483, retro_ggor_1484, retro_ggor_1783, retro_ggor_2365, retro_ggor_491, retro_ggor_517,
Loxodonta africana	ENSLAFG00000001910	5 retrocopies	retro_lafr_48, retro_lafr_515, retro_lafr_611, retro_lafr_881, retro_lafr_929,
Microcebus murinus	ENSMICG00000010381	4 retrocopies	retro_mmur_1160, retro_mmur_225, retro_mmur_320, retro_mmur_728,
Myotis lucifugus	ENSMLUG00000006865	1 retrocopy	retro_mluc_84,
Macaca mulatta	ENSMMUG00000012104	3 retrocopies	retro_mmul_2142, retro_mmul_2454, retro_mmul_946,
Mustela putorius furo	ENSMPUG00000002336	7 retrocopies	retro_mputfur_1099, retro_mputfur_1652, retro_mputfur_287, retro_mputfur_662, retro_mputfur_841, retro_mputfur_848, retro_mputfur_984,
Mus musculus	ENSMUSG00000027679	3 retrocopies	retro_mmus_1446, retro_mmus_3071, retro_mmus_3554,
Otolemur garnettii	ENSOGAG00000008754	11 retrocopies	retro_ogar_1214, retro_ogar_1334, retro_ogar_138, retro_ogar_1625, retro_ogar_1811, retro_ogar_2012, retro_ogar_2048, retro_ogar_2881, retro_ogar_301, retro_ogar_442, retro_ogar_718,
Ochotona princeps	ENSOPRG00000009256	5 retrocopies	retro_opri_1127, retro_opri_122, retro_opri_440, retro_opri_529, retro_opri_844,
Procavia capensis	ENSPCAG00000014950	2 retrocopies	retro_pcap_195, retro_pcap_25,
Pongo abelii	ENSPPYG00000014328	2 retrocopies	retro_pabe_2126, retro_pabe_44,
Rattus norvegicus	ENSRNOG00000049819	1 retrocopy	retro_rnor_2913,
Sus scrofa	ENSSSCG00000011770	2 retrocopies	retro_sscr_651, retro_sscr_891,
Ictidomys tridecemlineatus	ENSSTOG00000011508	1 retrocopy	retro_itri_552,
Tupaia belangeri	ENSTBEG00000015089	27 retrocopies	retro_tbel_1126, retro_tbel_1166, retro_tbel_1167, retro_tbel_1296, retro_tbel_1301, retro_tbel_1491, retro_tbel_1693, retro_tbel_1780, retro_tbel_2117, retro_tbel_2136, retro_tbel_2267, retro_tbel_2459, retro_tbel_266, retro_tbel_2830, retro_tbel_3233, retro_tbel_3303, retro_tbel_3556, retro_tbel_3716, retro_tbel_3814, retro_tbel_384, retro_tbel_3849, retro_tbel_3963, retro_tbel_4043, retro_tbel_42, retro_tbel_633, retro_tbel_833, retro_tbel_889,
Tarsius syrichta	ENSTSYG00000001611	3 retrocopies	retro_tsyr_112, retro_tsyr_174, retro_tsyr_312,
Tursiops truncatus	ENSTTRG00000014700	6 retrocopies	retro_ttru_1023, retro_ttru_1630, retro_ttru_1830, retro_ttru_662, retro_ttru_704, retro_ttru_962,
Vicugna pacos	ENSVPAG00000003387	1 retrocopy	retro_vpac_533,