RetrogeneDB ID: retro_cpor_577

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:29651951..29652653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000001236
• Aliases: None
• Description: None

Sequence

>retro_cpor_577
GAGACATCACCTTCACCATCACCAACATAAATGAGTCTTCCCCCACTGACCATGGAAGAGGCAGAGGATGAGAACTATGG
GGAGGATACAATTGAGTTGCTCAGAGGCGCAGGATAGATGAGATCATGACGGAACCAAAGTCTTGAGCTCAGTGAAAATT
TGCAGAGAACCATAGAGGAGCATGCAAATATCCTGTTTGGTTTTGTTAAGAAAAAGAAAGAAGAGGGCATTATTGACTCA
TCCAACAAAGAAGTTGTTGCTGAAGCAGAAAAACTAGATGTAAAACCCAAGAAGCCTCTTGTCCTAACTAAATTTTTTTT
AATGAGAAGATACAGAACAAATTTAGAAATACAGTTGCCATTTCCTCAGATTCTGTCACAAGAAAAAGATCAGTGGTAAC
ATCTTCATGATTTGGAGTATGTGGTGGTGATGCACCCAGCTCAGCTGCTCTGCAAGATCCTGAACATCTTGAAGATGTAC
TATGCATTCTTTTTAGAAAAGATCATCATCTGCTGGTCAGAAATGGCCTTTAAGGAATACATTTAAAAAGAACTTGCCTA
TGAGATTCGTGTCAAAGTGGAATCAATTATAAAATGTTTGAATGAGGCAGAGGAAGAATCCTCAGGAGCTGAAAATGATG
AAGATGAAAATATTGAGGTGGTTTACTCAAAGGCTGCCAGGGCACCAAAAGCTGAGTGTGTT

Alignment

ORF - retro_cpor_577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.82 %
• Parental protein coverage: 55.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ETPPPPPPSEMSPPPRAIEEEEDDDWGEDTTE-EAQRRRMDEIS-DHAKVLT-LSDDLERTIEERVNILF
          ET.P.P.P..MS.PP...EE.ED...GEDT.E..AQRRR.DEI..D..KVL..LS..L.RTIEE..NILF
Retrocopy ETSPSPSPT*MSLPPLTMEEAEDENYGEDTIE<VAQRRRIDEIM<DGTKVLS<LSENLQRTIEEHANILF

Parental  DFVKKKKEEGIIDSSDKEIVAEAERLDVKAMGPLVLTEVLF-NEKIR-EQIKKYRRHFLRFCHNNKKAQR
          .FVKKKKEEGIIDSS.KE.VAEAE.LDVK...PLVLT.....NEKI..EQI.KY..HFLRFC...KK...
Retrocopy GFVKKKKEEGIIDSSNKEVVAEAEKLDVKPKKPLVLTKXXX<NEKIQ<EQI*KYSCHFLRFC-HKKKISG

Parental  YL-LHGLECVVAMHQAQLLAKIPHILKEMYDADLLEEEVIISWSEKASKKYVSKELAKEIRVKAEPFIKW
          ...LH.LE.VV.MH.AQLL.KI..ILK.MY.A..LE...II.WSE.A.K.Y..KELA.EIRVK.E..IK.
Retrocopy NI<LHDLEYVVVMHPAQLLCKILNILK-MYYAFFLEK-IIICWSEMAFKEYI*KELAYEIRVKVESIIKC

Parental  LKEAEEESSGGEDEEEDENIEVVYSKTASVPKVETV
          L.EAEEESSG.E...EDENIEVVYSK.A..PK.E.V
Retrocopy LNEAEEESSGAEN-DEDENIEVVYSKAARAPKAECV

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	159.32 RPM
SRP017611_kidney	0.00 RPM	172.00 RPM
SRP017611_liver	0.00 RPM	115.26 RPM
SRP040447_lung	0.00 RPM	150.62 RPM
SRP040447_skeletal_muscle	0.00 RPM	167.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_577 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_577 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577 ,
Erinaceus europaeus	ENSEEUG00000015883	1 retrocopy	retro_eeur_288,
Echinops telfairi	ENSETEG00000015220	2 retrocopies	retro_etel_1843, retro_etel_991,
Homo sapiens	ENSG00000100664	1 retrocopy	retro_hsap_4782,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000,
Nomascus leucogenys	ENSNLEG00000016105	1 retrocopy	retro_nleu_1102,
Pongo abelii	ENSPPYG00000006169	1 retrocopy	retro_pabe_3722,
Pan troglodytes	ENSPTRG00000006753	1 retrocopy	retro_ptro_3183,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781, retro_rnor_2459,
Tursiops truncatus	ENSTTRG00000002384	1 retrocopy	retro_ttru_400,