RetrogeneDB ID: retro_cpor_804

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:11189275..11189735(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB4
• Ensembl ID: ENSCPOG00000012746
• Aliases: None
• Description: None

Sequence

>retro_cpor_804
CAACACCTAATGCAGTTCTGCCTTAAACTAGATAGACTTGCTGTTAAACTTCAGAGTGAATGCCATCCACATACTTGCAC
CCAGCTGACAGCAACTGAACAATGGATTTTTCTTTGTGCTGCTTATAAAACTCCAAGAGAGTGCTGTGCTATAGACTACA
CCAGACACACGCTCCATGGTGCTGTCTCCTGCTCAACAGCCATAAATATTTTCCCAGCAGGGTTAGCATAAAAGAATCAT
CTGCAGCAAAATTAGGATCCTTATGTCGTAGGATTTATAGAATATTTTCACCTGTTTATTTTCATCACCAGCAGATATTT
GATGAATATGAAAATGGAGCATTTTCATGTCATTGATTACTAAGTTAGTGATGAAATATAACCTGGTATCCAAGGATAAC
TCGATTTTACCAATTTTGGAAGAAGAAGTTCAGAATCCAGTTTCTGGGGAGAGTGAAGCG

Alignment

ORF - retro_cpor_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 68.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EHLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGA-ACLLNSNK
          .HL.QFCL.L..LAVKLQSECHP.TCTQ.TATEQWIFLCAA.KTP.EC.AIDYTRHTL.GA...LLNS.K
Retrocopy QHLMQFCLKLDRLAVKLQSECHPHTCTQLTATEQWIFLCAAYKTPRECCAIDYTRHTLHGA<CLLLNSHK

Parental  YFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCH-RFTKFVMKYNLMSKDNLIVP
          YFPSRVSIKESS.AKLGS.CRRIYRIFS..YFHH.QIFDEYEN..F.CH...TK.VMKYNL.SKDN.I.P
Retrocopy YFPSRVSIKESSAAKLGSLCRRIYRIFSPVYFHHQQIFDEYENGAFSCH<LITKLVMKYNLVSKDNSILP

Parental  ILEEEVQNSVSGESEA
          ILEEEVQN.VSGESEA
Retrocopy ILEEEVQNPVSGESEA

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	21.57 RPM
SRP017611_kidney	0.00 RPM	27.01 RPM
SRP017611_liver	0.00 RPM	16.80 RPM
SRP040447_lung	0.00 RPM	23.43 RPM
SRP040447_skeletal_muscle	0.00 RPM	29.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_804 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_804 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004020	2 retrocopies	retro_cjac_1960, retro_cjac_3238,
Cavia porcellus	ENSCPOG00000012746	2 retrocopies	retro_cpor_318, retro_cpor_804 ,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Gorilla gorilla	ENSGGOG00000009005	2 retrocopies	retro_ggor_733, retro_ggor_743,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Macaca mulatta	ENSMMUG00000016547	1 retrocopy	retro_mmul_829,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Otolemur garnettii	ENSOGAG00000000272	1 retrocopy	retro_ogar_2739,
Ochotona princeps	ENSOPRG00000016650	2 retrocopies	retro_opri_444, retro_opri_812,
Pongo abelii	ENSPPYG00000013047	6 retrocopies	retro_pabe_1943, retro_pabe_2021, retro_pabe_3600, retro_pabe_781, retro_pabe_795, retro_pabe_970,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Ictidomys tridecemlineatus	ENSSTOG00000021024	1 retrocopy	retro_itri_727,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,