RetrogeneDB ID: retro_cpor_1155

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_50:4790573..4791045(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSCPOG00000014532
• Aliases: None
• Description: None

Sequence

>retro_cpor_1155
GCCTATGGGAAAGACCACTATTCCAATGGCTTCTGTAGTGTACATGCTAAAACTATAAATGGGCAACAGACTACTGTCGC
GTCTGTTGAAAGCCACCAGTTCCAGCCTAAAAGTTTCTGGAGTGGTCACTGGAGATCAGAGTGGAAGTTCATCATCAACC
ACCTTGTAGAGCTCAGGTAGCTGGAGTACGCAAGATTCAGACTCATTATTATGAAGGTGTCAATGTTTAACTGGCTAGTT
GTAAAGATGTTCAAGATTCAGTAAATGTTTCAAATGAAGTCCAAACTGCTAAGCAGTTTACTAAGATCACAGAGAATACA
TAAAATGAATATCAGACAGCAATTAGTGAGAGTCATCAAACAATGTCAGACACCATGTTCGAAATCTTGCACCAGAAGTT
CCCAGTTACCTTCACCAAAATCAACAGAACAATATACTCAGCTCCAAGATTGGCAAAGAGATGCAGAATGCT

Alignment

ORF - retro_cpor_1155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 55.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AYVKDHYSNGFCTEVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTIT-PPT-AQVVGVLKIQV
          AY.KDHYSNGFC..V.AKTI.GQQT..A..ESHQFQPK.FW.G.WRSEWKF.I..PP..AQV.GV.KIQ.
Retrocopy AYGKDHYSNGFCS-VHAKTINGQQTTVASVESHQFQPKSFWSGHWRSEWKFIIN<PPCRAQVAGVRKIQT

Parental  HYYEDGNVQLVSHKDVQDSVNVSNEGQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTR
          HYYE..NV.L.S.KDVQDSVNVSNE.QTAK.F.KI.EN..NEYQTAISE..QTMSDT.F..L....PVT.
Retrocopy HYYEGVNV*LASCKDVQDSVNVSNEVQTAKQFTKITENT*NEYQTAISESHQTMSDTMFEILHQKFPVTF

Parental  TKID-WNKILSYKIGKEMQNA
          TKI...N.ILS.KIGKEMQNA
Retrocopy TKIN<QNNILSSKIGKEMQNA

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	15.13 RPM
SRP017611_kidney	0.00 RPM	42.61 RPM
SRP017611_liver	0.00 RPM	39.61 RPM
SRP040447_lung	0.00 RPM	55.51 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1155 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1155 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 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155 ,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,