RetrogeneDB ID: retro_cpor_10

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:3369251..3369938(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000019924
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NAA10
• Ensembl ID: ENSCPOG00000011495
• Aliases: None
• Description: None

Sequence

>retro_cpor_10
ATGAACATCCGCAATGCCCGGCCAGACGACTTGATGAACATGCAGCACTGCAACCTCCTCTGCCTGCCCGAGAACTACCA
GATGAAGTATTACTTCTACCACGGTCTCTCCTGGCCACAACTCTCCTACATCGCCGAAGACGAGGATGGAAAGGTCGTGG
GCTATGTCCTGGCCAAAATGGAGGAGGACCCTAACGATGTCGCCCATGGGCATATCACCTCGCTGGCCGTAAAGCGCTCA
CACCGGCGCCTTGGCCTGGCACAGAAGCTGATGGACCAGGCCTCGCGGGCCATGGTGGAGAACTTCGGTGCCAGGTACGT
GTCCCTGCACGTCAGGAAGAGTAACCGGGCGGCCTTGCACCTCTACTCTCACACCCTCAACTTCCAGGTCAATGAGGTGG
AGCCCAGATACTATGCGGATGGGGAGGATGCTTATGCGATGAGGCGGGATCTCTCACAGATGGCAGGTGAGCTGAGACGG
CAGCTGGAGCTGAAGAAGGGCGGGCATGTGGTACTGGGCTCCGGGGAAAACCAGGAGACCCACAGCGGCATATTTCCGGA
TTCGGAGAAGACCTGCCAGCAAGAGAGCCCAGCTGCCACAGATAGTGGCAGTGACACCAAGGAATCCAGCGAATCCACTG
AGAGCACTGATGTCCAAGACAGCTCAGAAGACTTGGATTCCATCTCC

Alignment

ORF - retro_cpor_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLSYIAEDENGKIVGYVLAKMEEDPDDVPHGHITSLAVKRSHRRLGLAQKLMDQASRAMIENFNAKYVSL
          QLSYIAEDE.GK.VGYVLAKMEEDP.DV.HGHITSLAVKRSHRRLGLAQKLMDQASRAM.ENF.A.YVSL
Retrocopy QLSYIAEDEDGKVVGYVLAKMEEDPNDVAHGHITSLAVKRSHRRLGLAQKLMDQASRAMVENFGARYVSL

Parental  HVRKSNRAALHLYSNTLNFQISEVEPKYYADGEDAYAMKRDLTQMAEELRRHLELKDKSRHVVLGVIENK
          HVRKSNRAALHLYS.TLNFQ..EVEP.YYADGEDAYAM.RDL.QMA.ELRR.LELK.K..HVVLG..EN.
Retrocopy HVRKSNRAALHLYSHTLNFQVNEVEPRYYADGEDAYAMRRDLSQMAGELRRQLELK-KGGHVVLGSGENQ

Parental  AESKGTPLPGPGEACREEKILAAEDSGGDSKDLSEVSETTESTDVKDSSEASDSAS
          ....G...P.....C..E...AA.DSG.D.K...E.SE.TESTDV.DSSE..DS.S
Retrocopy ETHSGI-FPDSEKTCQQES-PAATDSGSDTK---ESSESTESTDVQDSSEDLDSIS

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	0.06 RPM	21.91 RPM
SRP017611_kidney	0.31 RPM	24.92 RPM
SRP017611_liver	0.17 RPM	12.97 RPM
SRP040447_lung	0.00 RPM	25.80 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_10 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_10 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018457	1 retrocopy	retro_amel_162,
Bos taurus	ENSBTAG00000047702	1 retrocopy	retro_btau_177,
Canis familiaris	ENSCAFG00000019415	1 retrocopy	retro_cfam_167,
Callithrix jacchus	ENSCJAG00000014506	1 retrocopy	retro_cjac_132,
Cavia porcellus	ENSCPOG00000011495	1 retrocopy	retro_cpor_10 ,
Dipodomys ordii	ENSDORG00000002753	1 retrocopy	retro_dord_529,
Equus caballus	ENSECAG00000015203	1 retrocopy	retro_ecab_717,
Felis catus	ENSFCAG00000028705	1 retrocopy	retro_fcat_51,
Macropus eugenii	ENSMEUG00000006054	2 retrocopies	retro_meug_1787, retro_meug_554,
Myotis lucifugus	ENSMLUG00000014267	1 retrocopy	retro_mluc_152,
Mustela putorius furo	ENSMPUG00000008989	1 retrocopy	retro_mputfur_1424,
Pteropus vampyrus	ENSPVAG00000000463	1 retrocopy	retro_pvam_1225,
Sarcophilus harrisii	ENSSHAG00000005952	1 retrocopy	retro_shar_362,
Sus scrofa	ENSSSCG00000012791	1 retrocopy	retro_sscr_987,
Tursiops truncatus	ENSTTRG00000007455	1 retrocopy	retro_ttru_198,