RetrogeneDB ID: retro_cpor_23

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:43209498..43210587(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000023891
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000020712
• Aliases: None
• Description: None

Sequence

>retro_cpor_23
ATGGCGACGAGCTACAGTGTGAAGCCTGAAGTGTACAGTAGGCCCCACTGTGTTCCCGGGGGTGCCCCCAAAACCCGGAG
GCCAGACAACACTGCCTTCAAACAGCAACGGCTTCCCGCCTGGCAGCCCATCCTTACCGCAGGCACCGTGATGCCTTTCT
TTTTCCTCGTTGGCCTCCTCTTTACCGCCATTGGCATTGGCATCTTAATCACTTCCAACAGCATCCAAGAGATTGAGGTT
GATTACACTGGAACTGAGCTTTCCAGTCCCTGCAATAAGTGTCTGTCTCCATTTGTGGCACCTTGCATTTGTACCATTAA
CTTCACCCTGGAAGAAGCATTCAAGGGCAGTGTGTATATGTACTATGGACTGTCTAATTTCTATCAAAATCATCGTCATT
ATGTGAAATCTCGAGATGACAGCCAACTAAGTGGGGATACTAGGGCTTTGCTTAACCCCAGTAGTGAATGTGAGCCTTAT
CGAAGAGATGAAGACAAACCGATTGCTCCTTGTGGAGCAATCGCCAACAGTTTATTTAATGATACATTAGAGCTGTATCA
GATCACCAATGAATCTGACCCTACTCCAGTACCTATTCCTTTGAAAAAGAAAGGTATTGCTTGGTGGACAGATAAAAATG
TGAAATTTAGAAATCCTCCTGGAGAAGGAAGCCTGGAAGAACGATTTAAAGGCACAACAAAGCCACTAAACTGGCGTAAA
CCAGTGTATATGCTGGATTCTGAAGATGATGATAATGGATTCATCAACGAGGATTTGATTGTTTGGATGCGCACTGCAGC
ATTGCCTACTTTTCGTAAATTGTATCGTGTTATAGAACAGAAAAATGATTTAGAGCCAACTTTACCAGCTGGGCGATACT
ATTTGAATGTCACGTATAATTACCCTGTACATTCTTTCGATGGACGAAAAAGGATGATCTTGAGTACCATTTCATGGATG
GGAGGAAAAAACCCATTTTTGGCAATTGCTTACATCACCACTGGATCCATCTCCTTTCTTCTGGGAGTTGTAATGTTAGT
AATTAATCATAAATATCAAAGTGATGGTAACATTGGCGTTACTCTTTAG

Alignment

ORF - retro_cpor_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 98.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMNCNPKDEVDGGPPCAPGGAAKTRRPDNTAFKQQRLPAWQPILTAGTVLPTFFIVGLIFIPIGIGIFV
          MA.....K.EV...P.C.PGGA.KTRRPDNTAFKQQRLPAWQPILTAGTV.P.FF.VGL.F..IGIGI..
Retrocopy MATSYSVKPEVYSRPHCVPGGAPKTRRPDNTAFKQQRLPAWQPILTAGTVMPFFFLVGLLFTAIGIGILI

Parental  TSNNIREIEIDYTGTEPSSPCNKCLSSNVTPCVCTINFTLEKAFEGNVFMYYGLSNFYQNHRRYVKSRDD
          TSN.I.EIE.DYTGTE.SSPCNKCLS..V.PC.CTINFTLE.AF.G.V.MYYGLSNFYQNHR.YVKSRDD
Retrocopy TSNSIQEIEVDYTGTELSSPCNKCLSPFVAPCICTINFTLEEAFKGSVYMYYGLSNFYQNHRHYVKSRDD

Parental  SQLNGDPRALVNPSKECEPYRRNEDLPIAPCGAIANSMFNDTLELFLITNDSDPTPKPILLQRKGIAWWT
          SQL.GD.RAL.NPS.ECEPYRR.ED.PIAPCGAIANS.FNDTLEL..ITN.SDPTP.PI.L..KGIAWWT
Retrocopy SQLSGDTRALLNPSSECEPYRRDEDKPIAPCGAIANSLFNDTLELYQITNESDPTPVPIPLKKKGIAWWT

Parental  DKHVKFRNPPGEGTLEERFKGTTKPVNWPKPVYMLDSEDDNNGFINEDLIVWMRTAALPTFRKLYRLIER
          DK.VKFRNPPGEG.LEERFKGTTKP.NW.KPVYMLDSEDD.NGFINEDLIVWMRTAALPTFRKLYR.IE.
Retrocopy DKNVKFRNPPGEGSLEERFKGTTKPLNWRKPVYMLDSEDDDNGFINEDLIVWMRTAALPTFRKLYRVIEQ

Parental  TDDLHPTLPAGQYYLNITYNYPVHSFDGRKRMILSTISWMGGKNPFLGIAYITVGSISFLLGVVLLVINH
          ..DL.PTLPAG.YYLN.TYNYPVHSFDGRKRMILSTISWMGGKNPFL.IAYIT.GSISFLLGVV.LVINH
Retrocopy KNDLEPTLPAGRYYLNVTYNYPVHSFDGRKRMILSTISWMGGKNPFLAIAYITTGSISFLLGVVMLVINH

Parental  KYRNSSNTADTM
          KY....N...T.
Retrocopy KYQSDGNIGVTL

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	74.83 RPM
SRP017611_kidney	0.00 RPM	53.50 RPM
SRP017611_liver	0.00 RPM	42.74 RPM
SRP040447_lung	0.00 RPM	81.59 RPM
SRP040447_skeletal_muscle	0.00 RPM	43.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_23 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_23 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23 ,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,