RetrogeneDB ID: retro_cpor_803

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:9885495..9886006(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFF
• Ensembl ID: ENSCPOG00000011881
• Aliases: None
• Description: None

Sequence

>retro_cpor_803
GTTAGTGTGGCAGCGTTCCCTCTCCCACTGCTGCTGAGGTGGCGGAAGTTAGTCTAATTCAGTATGAAACGGAATTCACT
GAAGGTATTAGTAAAAGAATGAGGGTCTTGGAAAAATTAAAAGTAGCACAACCAAATGCTGACCTGGAAAAAGGATTCCA
AAAGGCGTTCCAAATGTGAATGTCATAATGCAAATTCCAGAGCGGACTGCTATAGCAAGAAATAATGAAGAAATTTCATT
TTCAAGACCTGCAGATCTTAACCTTATTCAGCCAAATCCTTTAAAACCTCTGACACTCAAAACAGCACCTTGTGTACCTA
CGTTAAACGAAAAATCACTAGATTTTTCAAGACTTAGACCTTGTCCAACCCCTCAGAATTATGAACATTTCTATATGGTT
TGCAGGCTAAAAAGACAGTACTTTGTGAGTGAAAATGCTATTTGCCAAAATGGACCTCTGATCAGAAATGATTCTTTGTA
TGGCATTTCAAATGTAGATGCAAAAAATGAA

Alignment

ORF - retro_cpor_803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.86 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSVAAF-PSPTAAEMAEISRIQYEMEYTEGISQRMRVPEKLKVAPPNADLEQGFQ-EGVPNASVIMQVPE
          VSVAAF.PSPTAAE.AE.S.IQYE.E.TEGIS.RMRV.EKLKVA.PNADLE.GFQ..GVPN..VIMQ.PE
Retrocopy VSVAAF<PSPTAAEVAEVSLIQYETEFTEGISKRMRVLEKLKVAQPNADLEKGFQ<KGVPNVNVIMQIPE

Parental  RIVVAVGNNEEISFSRPADLDLIQSTPLKPLALKTPPRVLTLSERPLDFLDLERPSPTPQNDEQIRAVGR
          R...A..NNEEISFSRPADL.LIQ..PLKPL.LKT.P.V.TL.E..LDF..L.RP.PTPQN.E....V.R
Retrocopy RTAIA-RNNEEISFSRPADLNLIQPNPLKPLTLKTAPCVPTLNEKSLDFSRL-RPCPTPQNYEHFYMVCR

Parental  LKRERSMSENAVRQNGQLVRNDSMWYRSDSAPRNK
          LKR....SENA..QNG.L.RNDS....S.....N.
Retrocopy LKRQYFVSENAICQNGPLIRNDSLYGISNVDAKNE

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	76.38 RPM
SRP017611_kidney	0.00 RPM	49.73 RPM
SRP017611_liver	0.00 RPM	30.08 RPM
SRP040447_lung	0.00 RPM	37.50 RPM
SRP040447_skeletal_muscle	0.00 RPM	52.29 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_803 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_803 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021319	2 retrocopies	retro_btau_1233, retro_btau_826,
Callithrix jacchus	ENSCJAG00000012973	1 retrocopy	retro_cjac_4058,
Cavia porcellus	ENSCPOG00000011881	1 retrocopy	retro_cpor_803 ,
Homo sapiens	ENSG00000168958	2 retrocopies	retro_hsap_3391, retro_hsap_347,
Microcebus murinus	ENSMICG00000013200	1 retrocopy	retro_mmur_1002,
Nomascus leucogenys	ENSNLEG00000013420	1 retrocopy	retro_nleu_1706,