RetrogeneDB ID: retro_cpor_1488

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:51364697..51365001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSCPOG00000005927
• Aliases: None
• Description: None

Sequence

>retro_cpor_1488
ATGCCTTAGCTAGTGGACTGTTACTTCATTGGCTGGTACAAAGCTGATGTCAAAGGAAACTTTGTGAAGACCACTGCATA
CTACAACATTCTAGATGATTAAGTGTCATCACATTAGCAGAATCTCATCCAGTTCTTAAAAGTGGAAAAACAATTAAAAG
TATTTCTCGTCAGATCAAAACCAACTTTAGAAGACTTTAGAACAAGGTTCTGGAAAATTTAAGTGGGGGCACAATTTCTA
CAGAACTTGACCTTTGTTCAAAATTTACTGTATACATGGAGAAGAATATACCATACCTAGCTGT

Alignment

ORF - retro_cpor_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.93 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPSLVDRYFTRWYKTDVKG-KPCEDHCILQHSNRICVITLAESHPVLKSGKTIKSISYQISTNCSRLQNK
          MP.LVD.YF..WYK.DVKG.K.CEDHCILQHS....VITLAESHPVLKSGKTIKSIS.QI.TN..RL.NK
Retrocopy MP*LVDCYFIGWYKADVKG<KLCEDHCILQHSR*LSVITLAESHPVLKSGKTIKSISRQIKTNFRRL*NK

Parental  V-SGKFKRG-AQFL-TELA-PLCKIYCSDGEEYTISSC
          V.SGKFK.G.AQFL.TEL..PL.KIYC..GEEYTI.SC
Retrocopy V<SGKFKWG<AQFL<TELD<PLFKIYCIHGEEYTIPSC

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	4.77 RPM
SRP017611_kidney	0.00 RPM	3.25 RPM
SRP017611_liver	0.00 RPM	6.31 RPM
SRP040447_lung	0.00 RPM	3.53 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1488 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1488 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488 ,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583,