RetrogeneDB ID: retro_cpor_1306

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_68:7778626..7779279(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP5
• Ensembl ID: ENSCPOG00000003467
• Aliases: None
• Description: None

Sequence

>retro_cpor_1306
ATGAATGGATTCTTCGGGAAAGAGAAACCCAGGGCTCCACCATCCAGCCTGACTGACTGCATTGGCATGGTGGACTGCAG
GGCAGGACCTACTGATAAGATTTTCCAGCTGGATGCCAAGCTAGTGAAGTACAAGGATCAAATCAAGAAGATGAGAGAAG
GTCCTGCAAAGAATTTGGTCAAGCAGGAAGCCTTGTGAGTTCCAAAATCAAAGCAGATGTATGAAAGGCAGTGGGGCAAC
CTCGCCCAACAATGCCTTAACATGGAACAAGTCAATTATACATTCAGTCATTGAAAGACACTAAGATCAGGGTGGATGCT
ATGAGACAGGGAGTAAAGGAAATGAAGAAAGCATACAAGGAAGTGAAAATTGACCAGATAGAGGATTTACAAGATCAACT
ACAGGATATGATGGAAGATGCAAATGAAATTCAGGAAGCACTGAGTCACAGTTATGGCAACCTAGCATTAGATGAAAATG
ACCTAGAAGCAGAGTTGAATGCACTGAGTGATAAGCTTCTGACTGATGAAGAGAGTTTTTATTTGGATGAAGCATCATCT
GCTCTTGCAATACCAGAAGGTGTTCCCACTGACACTAAAAACAAGGATGGAGTCCTGGTGGATGAATTCGGATTGTCACA
GATGCCTGCTTCA

Alignment

ORF - retro_cpor_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNRFFGKAKPKAPPPSLTDCIGTVDSRAESIDKKISRLDAELVKYKDQIKKMREGPAKNMVKQKALRVLK
          MN.FFGK.KP.APP.SLTDCIG.VD.RA...DK.I..LDA.LVKYKDQIKKMREGPAKN.VKQ.AL.V.K
Retrocopy MNGFFGKEKPRAPPSSLTDCIGMVDCRAGPTDK-IFQLDAKLVKYKDQIKKMREGPAKNLVKQEAL*VPK

Parental  QKRMYEQQRDNLAQQSFNMEQANYT-IQSLKDTKTTVDAMKQGVKEMKKAYKEVKIDQIEDLQDQLEDMM
          .K.MYE.Q..NLAQQ..NMEQ.NYT.IQSLKDTK..VDAM.QGVKEMKKAYKEVKIDQIEDLQDQL.DMM
Retrocopy SKQMYERQWGNLAQQCLNMEQVNYT<IQSLKDTKIRVDAMRQGVKEMKKAYKEVKIDQIEDLQDQLQDMM

Parental  EDANEIQEALSRSYGTPELDEDDLEAELDALGDELLADEDSSYLDEAASAPAIPEGVPTDTKNKDGVLVD
          EDANEIQEALS.SYG...LDE.DLEAEL.AL.D.LL.DE.S.YLDEA.SA.AIPEGVPTDTKNKDGVLVD
Retrocopy EDANEIQEALSHSYGNLALDENDLEAELNALSDKLLTDEESFYLDEASSALAIPEGVPTDTKNKDGVLVD

Parental  EFGLPQIPAS
          EFGL.Q.PAS
Retrocopy EFGLSQMPAS

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	35.03 RPM
SRP017611_kidney	0.00 RPM	61.03 RPM
SRP017611_liver	0.00 RPM	47.97 RPM
SRP040447_lung	0.00 RPM	35.49 RPM
SRP040447_skeletal_muscle	0.00 RPM	13.67 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1306 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1306 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 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012672	1 retrocopy	retro_chof_2045,
Callithrix jacchus	ENSCJAG00000008104	2 retrocopies	retro_cjac_2868, retro_cjac_4159,
Cavia porcellus	ENSCPOG00000003467	2 retrocopies	retro_cpor_1221, retro_cpor_1306 ,
Dipodomys ordii	ENSDORG00000006280	2 retrocopies	retro_dord_292, retro_dord_764,
Echinops telfairi	ENSETEG00000001424	1 retrocopy	retro_etel_2126,
Homo sapiens	ENSG00000086065	2 retrocopies	retro_hsap_4822, retro_hsap_494,
Microcebus murinus	ENSMICG00000012113	2 retrocopies	retro_mmur_369, retro_mmur_843,
Myotis lucifugus	ENSMLUG00000011045	1 retrocopy	retro_mluc_954,
Macaca mulatta	ENSMMUG00000020149	1 retrocopy	retro_mmul_2573,
Monodelphis domestica	ENSMODG00000004012	2 retrocopies	retro_mdom_2002, retro_mdom_595,
Mus musculus	ENSMUSG00000028419	1 retrocopy	retro_mmus_1469,
Nomascus leucogenys	ENSNLEG00000005158	2 retrocopies	retro_nleu_2197, retro_nleu_2420,
Otolemur garnettii	ENSOGAG00000000774	6 retrocopies	retro_ogar_2072, retro_ogar_2190, retro_ogar_2386, retro_ogar_2504, retro_ogar_2509, retro_ogar_916,
Pongo abelii	ENSPPYG00000019137	2 retrocopies	retro_pabe_239, retro_pabe_3750,
Pan troglodytes	ENSPTRG00000020857	2 retrocopies	retro_ptro_3210, retro_ptro_373,
Rattus norvegicus	ENSRNOG00000008672	1 retrocopy	retro_rnor_2614,
Ictidomys tridecemlineatus	ENSSTOG00000026573	1 retrocopy	retro_itri_424,
Tupaia belangeri	ENSTBEG00000003486	5 retrocopies	retro_tbel_1626, retro_tbel_1894, retro_tbel_2407, retro_tbel_3364, retro_tbel_3494,
Tursiops truncatus	ENSTTRG00000010575	1 retrocopy	retro_ttru_338,