RetrogeneDB ID: retro_cpor_301

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:22063320..22063959(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFT52
• Ensembl ID: ENSCPOG00000027175
• Aliases: None
• Description: None

Sequence

>retro_cpor_301
AAGCTGGCAGTGCTTGGCTCACATCACATGTTCAGTGATCAGTATTTGGATAAAGAAGAAAACAGCAAAATCATGGATGC
TATTTTCCAACGGCCCACAACAGGAGACATCCACCTGAATCAGACTGATGCTGAGTTGCCAGAGATCTCCAGTTACATGA
GGCTGCCTGACACTGCCACACTGTCAGACCAGTTACGAGTGTGTCTTCAGAGGGAGATGAGAACCCATGCGACTTTACCA
CCCTTTTCCATTTGTCTATTTACCAGCTGGATACCACCTCCATCCTCAAAGTCATCAAGGCTCATGAGCAGTTAGAAGTG
AAACACAAACCACTCCAGCTCATCCAACCTCAATTTGAGATGCCACTGGCTGCCCTTCAGCCTGCTCTTCCCCTCTTAGC
TTCAGCGAGTTGCCACGTCCTCCTCTGGAACTATTTGACTTAAACAAGTCATTTTCCTCTGAAAAGGCACAGCTTGCTCA
GATTGCCAATAAGTACACTGAAGAAGACCTAGAATTCTATGTCAGGAAGTGTGGTGACATTCTTGGAATAACCAGTAAGC
TACCAAAGGATCAACAGAATGCCAAACAAATCCTTGAGCACATCTCTTCCAAATGGTGGAATTCAAGAAACTGAACCAA

Alignment

ORF - retro_cpor_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.57 %
• Parental protein coverage: 50.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLAVLGSCHMFSDQYLDKEENSKIMDVVFQWLTTGDIHLNQIDAEDPEITDYTMLPDTATLSERLRVCLQ
          KLAVLGS.HMFSDQYLDKEENSKIMD..FQ..TTGDIHLNQ.DAE.PEI..Y..LPDTATLS..LRVCLQ
Retrocopy KLAVLGSHHMFSDQYLDKEENSKIMDAIFQRPTTGDIHLNQTDAELPEISSYMRLPDTATLSDQLRVCLQ

Parental  -EGDENPRDFTTLFDLSIYQLDTTSLLKVIKAYEQLNVKHEPLQLIQPQFETPLPALQPAV-FPPSFREL
          .EGDENP.DFTTLF.LSIYQLDTTS.LKVIKA.EQL.VKH.PLQLIQPQFE.PL.ALQPA...P.SF.EL
Retrocopy <EGDENPCDFTTLFHLSIYQLDTTSILKVIKAHEQLEVKHKPLQLIQPQFEMPLAALQPAL<SPLSFSEL

Parental  PPPPLELFDLDETFSSEKARLAQITNKCTEEDLEFYVRKCGDILGVTSKLPKDQQDAKHILEHI-FFQVV
          P.PPLELFDL...FSSEKA.LAQI.NK.TEEDLEFYVRKCGDILG.TSKLPKDQQ.AK.ILEHI..FQ.V
Retrocopy PRPPLELFDLNKSFSSEKAQLAQIANKYTEEDLEFYVRKCGDILGITSKLPKDQQNAKQILEHI<LFQMV

Parental  EFKKLNQ
          EFKKLNQ
Retrocopy EFKKLNQ

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	26.92 RPM
SRP017611_kidney	0.00 RPM	50.35 RPM
SRP017611_liver	0.00 RPM	13.36 RPM
SRP040447_lung	0.00 RPM	29.41 RPM
SRP040447_skeletal_muscle	0.00 RPM	32.28 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_301 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_301 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027175	1 retrocopy	retro_cpor_301 ,
Microcebus murinus	ENSMICG00000015182	1 retrocopy	retro_mmur_400,
Myotis lucifugus	ENSMLUG00000016664	1 retrocopy	retro_mluc_990,
Otolemur garnettii	ENSOGAG00000007699	1 retrocopy	retro_ogar_2343,
Takifugu rubripes	ENSTRUG00000014953	1 retrocopy	retro_trub_46,