RetrogeneDB ID: retro_cpor_550

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_19:35776489..35776842(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000009017
• Aliases: None
• Description: None

Sequence

>retro_cpor_550
ATGCAAACCATTGGGGCCCTGCTCCTGTCTCAGGCGTTGATTCACTGTTGTACCACGGGTCTGATGGGGCCTTCCTCAGC
CTCTTTCCTGAGCAGGTCCTAGGACCCAGCTAAACCACCCTCCAGCAGCGCCCCCCAACACCATGTGGCCAGGCTGGGCT
TCCAGACCAGCATGGTCTTCCTGGACATTGACTCAGCGGCCAAGTTTACTGGCGCTGGGCCCACCACAGTTGGCATGGCT
GGATCTGGGGCTGGCACTGGACCGTGTTTGGCAGCTGGATCATCAGTTATGCCAGGAACCCATCGCTCAACCAGCAACCC
TTCTCCTAGGCCACCTTGGACTTCACCCTGTCC

Alignment

ORF - retro_cpor_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 86.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQTTGALRLSPALIRCCTRGLIRPASASFLSRPQDPPKSPSSSAPQLQVARRDFQTSVVSRDIDTAAKFI
          MQT.GAL.LS.ALI.CCT.GL..P.SASFLSR..DP.K.PSSSAPQ..VAR..FQTS.V..DID.AAKF.
Retrocopy MQTIGALLLSQALIHCCTTGLMGPSSASFLSRS*DPAKPPSSSAPQHHVARLGFQTSMVFLDIDSAAKFT

Parental  GAGAATVGVAGSGAGIG-TVFGSLIIGYARNPSLKQQLFSYAILGFALS
          GAG..TVG.AGSGAG.G.TVFGS.II.YARNPSL.QQ.FS.A.L.F.LS
Retrocopy GAGPTTVGMAGSGAGTG<TVFGSWIISYARNPSLNQQPFS*ATLDFTLS

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	0.06 RPM	54.18 RPM
SRP017611_kidney	0.31 RPM	182.78 RPM
SRP017611_liver	0.00 RPM	79.09 RPM
SRP040447_lung	0.05 RPM	38.46 RPM
SRP040447_skeletal_muscle	0.01 RPM	269.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_550 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_550 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 28 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006341	1 retrocopy	retro_acar_9,
Bos taurus	ENSBTAG00000018339	3 retrocopies	retro_btau_1506, retro_btau_423, retro_btau_431,
Canis familiaris	ENSCAFG00000016880	5 retrocopies	retro_cfam_1583, retro_cfam_1621, retro_cfam_1882, retro_cfam_336, retro_cfam_647,
Callithrix jacchus	ENSCJAG00000007352	7 retrocopies	retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Cavia porcellus	ENSCPOG00000009017	2 retrocopies	retro_cpor_43, retro_cpor_550 ,
Cavia porcellus	ENSCPOG00000022889	3 retrocopies	retro_cpor_1495, retro_cpor_268, retro_cpor_492,
Equus caballus	ENSECAG00000019908	1 retrocopy	retro_ecab_463,
Felis catus	ENSFCAG00000002344	2 retrocopies	retro_fcat_1165, retro_fcat_1346,
Homo sapiens	ENSG00000159199	8 retrocopies	retro_hsap_1054, retro_hsap_1234, retro_hsap_1397, retro_hsap_1464, retro_hsap_2844, retro_hsap_2882, retro_hsap_597, retro_hsap_686,
Gorilla gorilla	ENSGGOG00000001626	8 retrocopies	retro_ggor_1083, retro_ggor_1125, retro_ggor_1388, retro_ggor_1998, retro_ggor_528, retro_ggor_589, retro_ggor_831, retro_ggor_967,
Loxodonta africana	ENSLAFG00000004537	2 retrocopies	retro_lafr_341, retro_lafr_522,
Macropus eugenii	ENSMEUG00000005744	2 retrocopies	retro_meug_1650, retro_meug_1973,
Myotis lucifugus	ENSMLUG00000011738	4 retrocopies	retro_mluc_1276, retro_mluc_1508, retro_mluc_1885, retro_mluc_2498,
Macaca mulatta	ENSMMUG00000013395	1 retrocopy	retro_mmul_173,
Mustela putorius furo	ENSMPUG00000015341	3 retrocopies	retro_mputfur_1575, retro_mputfur_479, retro_mputfur_497,
Mus musculus	ENSMUSG00000006057	5 retrocopies	retro_mmus_1523, retro_mmus_1726, retro_mmus_2128, retro_mmus_725, retro_mmus_829,
Nomascus leucogenys	ENSNLEG00000002718	6 retrocopies	retro_nleu_1082, retro_nleu_1475, retro_nleu_2074, retro_nleu_2219, retro_nleu_623, retro_nleu_777,
Oryctolagus cuniculus	ENSOCUG00000016225	2 retrocopies	retro_ocun_346, retro_ocun_375,
Otolemur garnettii	ENSOGAG00000011713	3 retrocopies	retro_ogar_1847, retro_ogar_2767, retro_ogar_531,
Pongo abelii	ENSPPYG00000008909	9 retrocopies	retro_pabe_1027, retro_pabe_1156, retro_pabe_1576, retro_pabe_1607, retro_pabe_2353, retro_pabe_2387, retro_pabe_537, retro_pabe_593, retro_pabe_879,
Pan troglodytes	ENSPTRG00000009364	8 retrocopies	retro_ptro_1273, retro_ptro_1926, retro_ptro_1950, retro_ptro_440, retro_ptro_491, retro_ptro_718, retro_ptro_847, retro_ptro_960,
Rattus norvegicus	ENSRNOG00000007235	5 retrocopies	retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Sus scrofa	ENSSSCG00000017544	1 retrocopy	retro_sscr_348,
Ictidomys tridecemlineatus	ENSSTOG00000013404	2 retrocopies	retro_itri_1604, retro_itri_560,
Tupaia belangeri	ENSTBEG00000003575	5 retrocopies	retro_tbel_2765, retro_tbel_3270, retro_tbel_3540, retro_tbel_387, retro_tbel_4002,
Tursiops truncatus	ENSTTRG00000008526	1 retrocopy	retro_ttru_279,
Vicugna pacos	ENSVPAG00000007653	1 retrocopy	retro_vpac_282,