RetrogeneDB ID: retro_cpor_1430

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_80:7067325..7067683(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL17
• Ensembl ID: ENSCPOG00000027536
• Aliases: None
• Description: None

Sequence

>retro_cpor_1430
CCTTGGTCCTGCATTCACTTGTTGCGAAATTGCTCACTGGGCTGATGTGACACGAGCGCATCAAGGCGACATGGGCAAGG
CTATAGAGATGCGGGGCTACATCAAGAAACTCATCAACTCTGGAAAAATGGGAAACACCAACAAATGAGCCGTGAGCATG
GCTGACTTCTGTATTATAGAGAAAAACTTGATTCCAAAGCTGTTTACAGTACTGGCCCCTTGGTACCAAGGTCAGAATGG
GGGTTACACAAGGATGGTGCAGGTTCCAAATCGAAACAAGCAGGATCGGGCAAAAATGGCAGTCATCAAATACAAAGGGA
ATTGCCTCCCATCCCAGCGAGACAGCAGCCTAGTACTT

Alignment

ORF - retro_cpor_1430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 70.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PESRIHLLRN-LLTGLVRHERIEATWARV-DEMRGYAEKLIDYGKMGDTNERAMRMADFWLTEKDLIPKL
          P.S.IHLLRN.LLTGL..HERI.ATWAR...EMRGY..KLI..GKMG.TN..A..MADF...EK.LIPKL
Retrocopy PWSCIHLLRN<LLTGLM*HERIKATWARL<IEMRGYIKKLINSGKMGNTNK*AVSMADFCIIEKNLIPKL

Parental  FKVLAPRFQGQNGGYTRMVQIPNRNKEDRAKMAVIEYKGNCLPPLPVPQRDSNLTL
          F.VLAP..QGQNGGYTRMVQ.PNRNK.DRAKMAVI.YKGNCLP.....QRDS.L.L
Retrocopy FTVLAPWYQGQNGGYTRMVQVPNRNKQDRAKMAVIKYKGNCLP----SQRDSSLVL

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	0.12 RPM	11.04 RPM
SRP017611_kidney	0.31 RPM	21.98 RPM
SRP017611_liver	0.00 RPM	17.54 RPM
SRP040447_lung	0.03 RPM	16.49 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.30 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1430 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1430 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027536	1 retrocopy	retro_cpor_1430 ,
Macropus eugenii	ENSMEUG00000013588	1 retrocopy	retro_meug_1822,
Myotis lucifugus	ENSMLUG00000001144	2 retrocopies	retro_mluc_2368, retro_mluc_679,
Mustela putorius furo	ENSMPUG00000005449	1 retrocopy	retro_mputfur_125,
Rattus norvegicus	ENSRNOG00000019497	1 retrocopy	retro_rnor_1979,
Sus scrofa	ENSSSCG00000024693	1 retrocopy	retro_sscr_217,
Ictidomys tridecemlineatus	ENSSTOG00000003313	3 retrocopies	retro_itri_1019, retro_itri_1156, retro_itri_240,