RetrogeneDB ID: retro_cpor_1362

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_71:8072033..8072567(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FRG1
• Ensembl ID: ENSCPOG00000022277
• Aliases: None
• Description: FSHD region gene 1 [Source:HGNC Symbol;Acc:3954]

Sequence

>retro_cpor_1362
GTTTTTTAAACAGGCAGCACCCATAGAGAAGTTGATGAAGGTCTTAGTCCTCCAGAGAAGTTTACTGCTGCCAAACTGTC
TGATTCTACAACTTTCCTGAAATCTGGCTATGGAAATATCTTGGTATCAATTCAGATGGACTTCTTGTTGGACATTCAGA
TGCCTTTGAAACAAGCGACCAGTGGGAACCAGAGTTTCCAGATGGGAAATTGGCCTTATTGACCTCAAATAGTTGCTTTA
TTAGATGCAATGAAACAGGCGATAAAGAAGCAAAAAAGGAAAACAACAAGACAAGAAGAAATGATAAAGATTAGAACCTG
AGCTGAAAGGGAAACCAAGAAAAAGATGACACCCCAGAAGACAAAGGAAAGCAAAACAGTGTGGAATCAACCATGTAAAA
AAAAAAATCAGAATTTCCAAGATCATGAATTCAAAATCAGCAAAGAAGACAGTAAAATTCTTTAAAAGGCATGGAAAAGT
GGACGATTCACATCTGACAGGAGAGACAAGATGAAAGATATTGCAAATGACCAG

Alignment

ORF - retro_cpor_1362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.56 %
• Parental protein coverage: 68.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFTLGAPHKEVDEGPSPPEQFTAVKLSDSRIALKSGYG-KYLGINSDGLVVGRSDAIGPREQWEPVFQDG
          .F..G..H.EVDEG.SPPE.FTA.KLSDS...LKSGYG.KYLGINSDGL.VG.SDA.....QWEP.F.DG
Retrocopy VF*TGSTHREVDEGLSPPEKFTAAKLSDSTTFLKSGYG<KYLGINSDGLLVGHSDAFETSDQWEPEFPDG

Parental  KMALLASNSCFIRCNEAGDIEAKS-KTAGEEEMIKIRSCAERETKKKDDIPEEDKGNVKQCEINYVKKFQ
          K.ALL.SNSCFIRCNE.GD.EAK..KT...EEMIKIR..AERETK.K...P...K..............Q
Retrocopy KLALLTSNSCFIRCNETGDKEAKK>KTTRQEEMIKIRT*AERETK-KKMTPQKTKESKTVWNQPCXXXXQ

Parental  SFQDHKLKISKEDSKILKKARKDGFLHETLLDRRAKLKADR
          .FQDH..KISKEDSKIL.KA.K.G.......D.......D.
Retrocopy NFQDHEFKISKEDSKIL*KAWKSGRFTSDRRDKMKDIANDQ

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	12.37 RPM
SRP017611_kidney	0.00 RPM	27.32 RPM
SRP017611_liver	0.00 RPM	18.28 RPM
SRP040447_lung	0.00 RPM	20.93 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1362 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1362 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022277	7 retrocopies	retro_cpor_1349, retro_cpor_1350, retro_cpor_1359, retro_cpor_1361, retro_cpor_1362 , retro_cpor_1363, retro_cpor_864,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464,
Otolemur garnettii	ENSOGAG00000005749	2 retrocopies	retro_ogar_1523, retro_ogar_2535,
Pan troglodytes	ENSPTRG00000016671	1 retrocopy	retro_ptro_2930,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,