RetrogeneDB ID: retro_cpor_1030

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:12551104..12551616(-)
• Located in intron of: ENSCPOG00000022250

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000011651
• Aliases: None
• Description: None

Sequence

>retro_cpor_1030
GGCCAGTGGACCAGGTTGAAGACATTTGTCACCACCAGGACTACAACAGTCATGTTGGTCTGGGTGTAATAAAGTGCTCT
AAGGAAGCAGCCACTGCCATTCGGGGGACCATCATCCTGGCCAAGCTCTCCACTGTCCCTGCACAGAGAGGCTACTGGAG
GACAGAACTGGCAAGCCCCACACTGTCTCTTGCAAGGTGAGGGACTGCTGTGACTCTGGGTTGGCACGTCTGATCCTTTC
CCCTACAGGCACTGGCATCATCTCAGGCGCTATGCCCAAGAAGCTGCTGCTGATGACTGGTACTAACTCTGCCAGGGGCT
GCAGTGCCACTCTGAGCAATGTCACTAAGGCCACTTTAATGCTATCACCGAGACCTATAGCTACTTGACCCATAGGCTTT
GGAAAGATACCGTGTTCACCATTCTCCCTACCAGGAATTCAGCGACCATTTTGTGAAAACACACACCCAAGCCTCTGCCC
AGAGGACTCAAGCTTCAACAGTAGCTACAACA

Alignment

ORF - retro_cpor_1030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.11 %
• Parental protein coverage: 63.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GQRTRFKAFVAIG-DYNGHVGLGV-KCSKEVATAIRGAIILAKLSIVPVRRGYWGNKI-GKPHTVPCKVT
          GQ.TR.K.FV....DYN.HVGLGV.KCSKE.ATAIRG.IILAKLS.VP..RGYW.....GKPHTV.CKV.
Retrocopy GQWTRLKTFVTTR<DYNSHVGLGVIKCSKEAATAIRGTIILAKLSTVPAQRGYWRTEL<GKPHTVSCKVR

Parental  GRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT-FDAISKTYSYLTPD
          ..C.S.L.RLI..P.GTGI.S...PKKLL.M.G......SARGC.ATL.N..KAT.F.AI..TYSYLT..
Retrocopy DCCDSGLARLILSPTGTGIISGAMPKKLLLMTGTN----SARGCSATLSNVTKAT<FNAITETYSYLTHR

Parental  LWKETVFT-KSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
          LWK.TVFT..SPYQEF.DH.VKTHT..S.QRTQA..VATT
Retrocopy LWKDTVFT<HSPYQEFSDHFVKTHTQASAQRTQASTVATT

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	0.40 RPM	223.91 RPM
SRP017611_kidney	0.10 RPM	288.62 RPM
SRP017611_liver	0.00 RPM	204.01 RPM
SRP040447_lung	0.25 RPM	346.71 RPM
SRP040447_skeletal_muscle	0.01 RPM	660.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1030 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1030 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 17 parental genes, and 124 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Ailuropoda melanoleuca	ENSAMEG00000007366	1 retrocopy	retro_amel_305,
Bos taurus	ENSBTAG00000009535	7 retrocopies	retro_btau_1236, retro_btau_1420, retro_btau_1656, retro_btau_317, retro_btau_590, retro_btau_661, retro_btau_956,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030 , retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Dipodomys ordii	ENSDORG00000007375	18 retrocopies	retro_dord_163, retro_dord_206, retro_dord_215, retro_dord_284, retro_dord_392, retro_dord_445, retro_dord_465, retro_dord_499, retro_dord_500, retro_dord_505, retro_dord_568, retro_dord_571, retro_dord_572, retro_dord_683, retro_dord_703, retro_dord_711, retro_dord_723, retro_dord_89,
Equus caballus	ENSECAG00000009065	7 retrocopies	retro_ecab_1025, retro_ecab_1105, retro_ecab_509, retro_ecab_632, retro_ecab_876, retro_ecab_892, retro_ecab_949,
Loxodonta africana	ENSLAFG00000004696	11 retrocopies	retro_lafr_1072, retro_lafr_1092, retro_lafr_1103, retro_lafr_174, retro_lafr_284, retro_lafr_327, retro_lafr_376, retro_lafr_75, retro_lafr_801, retro_lafr_812, retro_lafr_917,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Procavia capensis	ENSPCAG00000002090	2 retrocopies	retro_pcap_251, retro_pcap_433,
Pteropus vampyrus	ENSPVAG00000016704	8 retrocopies	retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34, retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tursiops truncatus	ENSTTRG00000011393	12 retrocopies	retro_ttru_1341, retro_ttru_1346, retro_ttru_1414, retro_ttru_149, retro_ttru_1762, retro_ttru_1816, retro_ttru_37, retro_ttru_375, retro_ttru_419, retro_ttru_650, retro_ttru_719, retro_ttru_872,
Vicugna pacos	ENSVPAG00000006867	6 retrocopies	retro_vpac_114, retro_vpac_164, retro_vpac_220, retro_vpac_354, retro_vpac_379, retro_vpac_518,