RetrogeneDB ID: retro_cpor_710

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:26990480..26990947(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAX
• Ensembl ID: ENSCPOG00000010172
• Aliases: None
• Description: None

Sequence

>retro_cpor_710
GATGACATCGCGGTGAAGAGCCACAAAGAGCAACCAGGTTTCAGTCTACAGCTGACAAATGGACTCATCAGGATGCACGG
GAATGAAAACGTAGGCACCACATCAAACACAGCTTTCAAAGTTTGCAGGACTCAGTTCCATCATGCCAAGGAGAGAAGGC
ATCCCAGGCCCAAATCCTGGACAAAGCCACAGAATATATCCAGGGCATGCGAAGGGAAAACCACACACACCAGCAAGATA
TTGATAACCTCAAGCAGCAGAATGCTCTTCTGGAGCAGTGAAGTCCGTGCACTGGAGAAAATGAGGTCAAGCGCCCAACT
GTAGAGCAACTACCCCTCCTCAGACAACAGCCTCTGCACCAGCTCCAAGGCCAGCACCACCTCTGCCTTAAGTGGGGCTC
CGACTCCAGCTTGGCCTCAGAGCCTGAAGAGCCCCAGAGCAGGAAGAAACTCAGGATGGAGGCCAGC

Alignment

ORF - retro_cpor_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.73 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDIEVESDEEQP-RFQSAADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQY
          DDI.V.S..EQP.RFQS.ADK..H..A.E.KRR.HIK.SF.SL.DSVPS.QGEKAS.AQILDKATEYIQ.
Retrocopy DDIAVKSHKEQP<RFQSTADKWTHQDARE*KRRHHIKHSFQSLQDSVPSCQGEKASQAQILDKATEYIQG

Parental  MRRKNHTHQQDIDDLKRQNALLEQ-QVRALEKARSSAQLQTNYPSSDSSLYTNSKGSTISAFDG-GSDSS
          MRR.NHTHQQDID.LK.QNALLEQ..VRALEK.RSSAQL..NYPSSD.SL.T.SK.ST.SA..G.GSDSS
Retrocopy MRRENHTHQQDIDNLKQQNALLEQ>EVRALEKMRSSAQL*SNYPSSDNSLCTSSKASTTSALSG<GSDSS

Parental  SESEPEEPQSRKKLRMEAS
          ..SEPEEPQSRKKLRMEAS
Retrocopy LASEPEEPQSRKKLRMEAS

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	23.01 RPM
SRP017611_kidney	0.00 RPM	17.59 RPM
SRP017611_liver	0.00 RPM	7.70 RPM
SRP040447_lung	0.00 RPM	31.88 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.28 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_710 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_710 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 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003472	2 retrocopies	retro_amel_1261, retro_amel_1606,
Canis familiaris	ENSCAFG00000016212	2 retrocopies	retro_cfam_1179, retro_cfam_1325,
Callithrix jacchus	ENSCJAG00000019702	2 retrocopies	retro_cjac_2057, retro_cjac_2556,
Cavia porcellus	ENSCPOG00000010172	1 retrocopy	retro_cpor_710 ,
Erinaceus europaeus	ENSEEUG00000003973	3 retrocopies	retro_eeur_216, retro_eeur_344, retro_eeur_37,
Echinops telfairi	ENSETEG00000002967	1 retrocopy	retro_etel_1294,
Felis catus	ENSFCAG00000010347	1 retrocopy	retro_fcat_278,
Macaca mulatta	ENSMMUG00000004341	1 retrocopy	retro_mmul_1648,
Mustela putorius furo	ENSMPUG00000006859	3 retrocopies	retro_mputfur_1218, retro_mputfur_1615, retro_mputfur_192,
Mus musculus	ENSMUSG00000059436	8 retrocopies	retro_mmus_2891, retro_mmus_2892, retro_mmus_2893, retro_mmus_2894, retro_mmus_2991, retro_mmus_2992, retro_mmus_2993, retro_mmus_2994,
Nomascus leucogenys	ENSNLEG00000014373	1 retrocopy	retro_nleu_1122,
Ochotona princeps	ENSOPRG00000016245	1 retrocopy	retro_opri_945,
Pongo abelii	ENSPPYG00000005911	1 retrocopy	retro_pabe_3097,
Rattus norvegicus	ENSRNOG00000008049	3 retrocopies	retro_rnor_1653, retro_rnor_1877, retro_rnor_2369,
Ictidomys tridecemlineatus	ENSSTOG00000028142	1 retrocopy	retro_itri_42,
Tupaia belangeri	ENSTBEG00000012645	1 retrocopy	retro_tbel_3407,