RetrogeneDB ID: retro_cpor_1386

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:2046064..2046543(+)
• Located in intron of: ENSCPOG00000005725

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABT1
• Ensembl ID: ENSCPOG00000008937
• Aliases: None
• Description: None

Sequence

>retro_cpor_1386
ATGTTGGCTGGGGGATCTGAGCTAGTGACAGAGCAGGAGTTTCTGGAAGGGACAGAAAAATCAGAGGTGGAGAAGCAGGA
AGAAGCCAAAGAAGAGGCTCAAGGCAGCAAGAAGCAGGTCGTGCCAGGTATCGCATACATGGGTCACATCCCACGTGCTT
CCGACCCCTACACACACACAAGCTCTGCAGGGCCTACGGGGAGGTCAGATGCATGTTCTTTCAGGCTGAGGACGGGTTTG
TGAAGGAGGCAGCAGTGGCCTTGAGAGAAAAAAAGGGATCCAAGTACAGCAAGGACTATATCGAGGGCTGGATGGAGTTC
TAGGATTCGCACAGAGTCAAGCTCATGGCCGAGTCTGTACAACACGCCCATGGGTGTCTACAGGTGCAACCCCTTCTGCT
ATGACTTGTGGAACTCAAGTATTTGTACTGCCTTACTTAGTCCCACCTCAGGGAACACCTTGCCTTTGAGTGCCAGTTA

Alignment

ORF - retro_cpor_1386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 60.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSAGGSEAATELEATDEKSEAE-EEQEEPREAAHGSKKRVVPGIVYLGHIPPR-FRPLHVRNLLSAYGEV
          M.AGGSE..TE.E........E.E.QEE..E.A.GSKK.VVPGI.Y.GHIP...FRPLH...L..AYGEV
Retrocopy MLAGGSELVTEQEFLEGTEKSEVEKQEEAKEEAQGSKKQVVPGIAYMGHIPRA<FRPLHTHKLCRAYGEV

Parental  GRVFFQAEDRFVRRKKKAAVASGGKKGSKYSKDYTEGWVEFRDKRIAKRVAASLHNT-PMGSRRRSP-FC
          ...FFQAED.FV...K.AAVA...KKGSKYSKDY.EGW.EF.D....K..A.S.....P..S....P.FC
Retrocopy RCMFFQAEDGFV---KEAAVALREKKGSKYSKDYIEGWMEF*DSHRVKLMAESVQHA<PWVSTGATP<FC

Parental  YDLWN-LKYLHRFTWSHLSEHLAFERQV
          YDLWN.LKYL...T.SHL.EHLAFE.Q.
Retrocopy YDLWN<LKYLYCLT*SHLREHLAFECQL

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	0.46 RPM	7.30 RPM
SRP017611_kidney	0.42 RPM	7.64 RPM
SRP017611_liver	0.26 RPM	5.09 RPM
SRP040447_lung	0.71 RPM	11.00 RPM
SRP040447_skeletal_muscle	0.14 RPM	8.84 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1386 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1386 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005188	1 retrocopy	retro_chof_1748,
Cavia porcellus	ENSCPOG00000008937	1 retrocopy	retro_cpor_1386 ,
Gorilla gorilla	ENSGGOG00000024149	1 retrocopy	retro_ggor_2106,
Macaca mulatta	ENSMMUG00000006914	1 retrocopy	retro_mmul_1959,
Otolemur garnettii	ENSOGAG00000026316	1 retrocopy	retro_ogar_2895,
Pongo abelii	ENSPPYG00000016335	1 retrocopy	retro_pabe_2541,
Rattus norvegicus	ENSRNOG00000017585	1 retrocopy	retro_rnor_841,
Sarcophilus harrisii	ENSSHAG00000003493	1 retrocopy	retro_shar_97,