RetrogeneDB ID: retro_cpor_1219

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_58:7559077..7559712(-)
• Located in intron of: ENSCPOG00000004829

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL47
• Ensembl ID: ENSCPOG00000002312
• Aliases: None
• Description: None

Sequence

>retro_cpor_1219
GTTTCTCTTAGATTGTCATCTAAGGATGCATCAAATGTCACATCCTTTCCCACTGTAGATTACTTCATACCACACTGTCA
AGAAAAGGACTGGAATAATATTTTGATGACCCAAAGAATTGGGGGCAAGAAAAAGTAGAACCTGGAGCTGCATGGTCCTG
TCAGCAATTAAGGAACAAAAGTGATGAAGATTTACATCAACTTTGGTGTGAGTACTGAAAGAAAGAAGCATGCTTCTAAC
CTAGAACAGGAGTCCAGGCGGCAGAGGTTACCAATGCCAAGTCCAGAAAGGTTAGAAAGCTAGCTGATTCCATGGATACA
TTAAAGATGTCCAGTAGAAAAGATGCTTTAAGGCTTCTACAGAGTGCTCAAGAAAAAGCTAGACCCAGTGCTCAAAGAGA
CATCTTTGCAAGAATCATTTGACACAAGTTCAGGCAGTGGTCTATATCTCAGCACCTAAATAAAAGATGCAACAGGAAAT
AATTTTTTGCAGTGTCTTATGAGGATCATTTTGTTAGACTGAGAACTGAGAGACAAGCCCGCAATGAAGGAGTAAAGAAA
AGTTAGGAGAAAAAATAACACAAAGGTCTGCACAAAAAGTTTCCACATCTTGCTGAAGCCCAGAAGTTGAGTCTT

Alignment

ORF - retro_cpor_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.64 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VSLNLFSKNAPDVTSF-HQCKLLHTTLSRKGLEEFFDDPKNWGQEKVKSGAAWTCQQLRNKSNEDLHKLW
          VSL.L.SK.A..VTSF...C.LLHTTLSRKGLE..FDDPKNWGQEKV..GAAW.CQQLRNKS.EDLH.LW
Retrocopy VSLRLSSKDASNVTSF<SHCRLLHTTLSRKGLE*YFDDPKNWGQEKVEPGAAWSCQQLRNKSDEDLHQLW

Parental  YV-LLKERNMLLT-LEQEAKRQSLPMPSPERLE-KVVESMDALDKVVQEREDALRLLQTGQERARPGAWR
          ....LKER.MLLT.LEQE..RQ.LPMPSPERLE.K...SMD.L......R.DALRLLQ..QE.ARP.A..
Retrocopy CE<VLKERSMLLT<LEQESRRQRLPMPSPERLE<KLADSMDTLK--MSSRKDALRLLQSAQEKARPSA-Q

Parental  RDIFGRIIWHKFKQWPIPWYLNKRYNRKRFFAMPYVDHFVRLRLEKQARIKARKASLEKKKEKALQEKFP
          RDIF.RII.HKF.QW.I...LNKR.NRK.FFA..Y.DHFVRLR.E.QAR....K.S.EKK..K.L..KFP
Retrocopy RDIFARII*HKFRQWSISQHLNKRCNRK*FFAVSYEDHFVRLRTERQARNEGVKKS*EKK*HKGLHKKFP

Parental  HLAEAQKSSL
          HLAEAQK.SL
Retrocopy HLAEAQKLSL

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	0.58 RPM	6.33 RPM
SRP017611_kidney	0.10 RPM	8.58 RPM
SRP017611_liver	0.13 RPM	8.57 RPM
SRP040447_lung	0.00 RPM	8.10 RPM
SRP040447_skeletal_muscle	0.07 RPM	6.99 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1219 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1219 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011380	1 retrocopy	retro_cfam_1085,
Cavia porcellus	ENSCPOG00000002312	2 retrocopies	retro_cpor_1219 , retro_cpor_885,
Felis catus	ENSFCAG00000031548	1 retrocopy	retro_fcat_235,
Macropus eugenii	ENSMEUG00000012649	2 retrocopies	retro_meug_1039, retro_meug_146,
Monodelphis domestica	ENSMODG00000021301	3 retrocopies	retro_mdom_1361, retro_mdom_1879, retro_mdom_562,
Mustela putorius furo	ENSMPUG00000017214	1 retrocopy	retro_mputfur_495,
Mus musculus	ENSMUSG00000037531	3 retrocopies	retro_mmus_1976, retro_mmus_1986, retro_mmus_2753,
Otolemur garnettii	ENSOGAG00000016957	2 retrocopies	retro_ogar_1900, retro_ogar_3015,
Pteropus vampyrus	ENSPVAG00000004284	1 retrocopy	retro_pvam_150,
Rattus norvegicus	ENSRNOG00000011639	2 retrocopies	retro_rnor_1829, retro_rnor_2523,
Sorex araneus	ENSSARG00000006898	2 retrocopies	retro_sara_269, retro_sara_721,
Tursiops truncatus	ENSTTRG00000008909	1 retrocopy	retro_ttru_420,