RetrogeneDB ID: retro_cpor_1498

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:35036487..35036958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABHD10
• Ensembl ID: ENSCPOG00000005650
• Aliases: None
• Description: None

Sequence

>retro_cpor_1498
GGCTGGGCAGCCTTCTCTTTTGGCCCCCACCATGTCCAGGATGCATTTCTAATGCTGAAGCCCCAGGGGATGCCCCGGGT
GACTCCCAGCTTGCAGACAAAAGACATGTTCAACTTCCTTAATTGACCGGACCTTCCAAAAATGGCTTCTAAGATTAAAA
AGAAAAATCCAGGAGTTATCTTCATCCCTGGCTACATCTCTAAAATGAATGGCACGAAAGAATTGGTGACTAAGGAATTT
TGCAAATCTTTAGAGCTTGTCTGTACAGGGTTTGATTACTCAGGAGTTGGAAAGTCAGAGGGTGATTTAGAAGAATGCAT
GGTGGGGAAATGAAGAAAAGATCTTCTTTTCATAATTGCTGATATGGCTGTAGGACCACAGATACTGGCTGGATCTAGCC
TTAGTGGGTGGCTGATGCTTTATGTTGCAATTGCACAACCAGAAAAGGCCATGGCTCTTGTTGGTGTAGCT

Alignment

ORF - retro_cpor_1498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.0 %
• Parental protein coverage: 51.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQATASFG-HYHNLSAPTLKSQRV-PWRFPVCRQKTS-FSFLNRPDLPKLAYKRLNGKSPGVIFIPGYIS
          G.A..SFG.H........LK.Q...P...P.CRQKT..F.FLN.PDLPK.A.K....K.PGVIFIPGYIS
Retrocopy GWAAFSFGPHHVQDAFLMLKPQGM>PG*LPACRQKTC<FNFLN*PDLPKMASK-IKKKNPGVIFIPGYIS

Parental  NMNGTKALAIEEFCKSLGHAYIRFDYSGVGNSEGNLEECTVGKWRKDILSIIDDIAVGPQILVGSSLGGW
          .MNGTK.L...EFCKSL......FDYSGVG.SEG.LEEC.VGK.RKD.L.II.D.AVGPQIL.GSSL.GW
Retrocopy KMNGTKELVTKEFCKSLELVCTGFDYSGVGKSEGDLEECMVGK*RKDLLFIIADMAVGPQILAGSSLSGW

Parental  LMLHAAIARPEKVMALVGVA
          LML..AIA.PEK.MALVGVA
Retrocopy LMLYVAIAQPEKAMALVGVA

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	8.51 RPM
SRP017611_kidney	0.00 RPM	17.48 RPM
SRP017611_liver	0.00 RPM	27.64 RPM
SRP040447_lung	0.00 RPM	5.75 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.22 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1498 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1498 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020230	1 retrocopy	retro_cjac_2973,
Cavia porcellus	ENSCPOG00000005650	1 retrocopy	retro_cpor_1498 ,
Dipodomys ordii	ENSDORG00000014818	1 retrocopy	retro_dord_28,
Felis catus	ENSFCAG00000029739	1 retrocopy	retro_fcat_176,
Ochotona princeps	ENSOPRG00000009517	1 retrocopy	retro_opri_1051,
Tursiops truncatus	ENSTTRG00000016358	1 retrocopy	retro_ttru_778,