RetrogeneDB ID: retro_cpor_790

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_28:4725327..4726326(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PM20D2
• Ensembl ID: ENSCPOG00000010921
• Aliases: None
• Description: None

Sequence

>retro_cpor_790
ATGAAACCTGGCGAGGAGCGCCCAGTGCAGTGTGGTGCATGCGATGGTGTCTCTGAGTTGGAGCTACAGGAGGTCCTAAA
GCTGTGTGCTGCAGAACACATGGATTAAGCAGTTGAATGGCTGGGAGCCCTGACCCGTGCCATCTGGAGCGAGCCCGAGC
TGGCTTACGAGGAGCACCATGCCCATGGCCTGCTGACACGCTTCTTTGAGCAGGAGTCACCGCCACGTCCAGGGCCCTGC
AGCCGCACCACCAATTGCCCACAGCCTTCCACGCCGCTGAATGGGCACCTCCGGGGGCCAGCGCGCCAGGGCGCTGAAGT
GCACGCTGCTGCTGGCTTTCCTCTGAGAGTAAAGACGCGCTGCCCTGCATCACCTACACCTGCAGCCACAACTTCATCGC
CGAGATCCAAACTAAAGCTGCACTGGGGCTGAGGGCAGCCCTGGAGAGCCTCCCTGGGCCGCCACAGCCTGTGAAGGTAA
TTGTCTTGGGAACCCCTGCCGAAGAAGATGGTGGTGGCAAAATTGATCTAATTGAAGCAGGTGCTTTTAAGAACCTTAAT
GTTGTATTTATGGCCCATACCTCCCAAGAGAATGCAGCTTAGCTACAGGATGTGGCTGAACATGATGTGACTGTGAAAAA
CTATGGAAAGGCTGCTGCATAACCCTGAGAAGGAGTAAGTGCTTTAAATGCTGCTGTTCTTGCCTACAACAATGTATCTG
TGTTAAGACAGCAAATGAAACCAACCTGGAGAGTTCATGGTATAATAAAAAATGGTGGTAAACCCCAGCATCATTCCCTC
TTATTCTGAATTAATTTGCTACTTCCATGCACCCTCAATGAAAGAACTTCAAGGTTTGTCCAAAAAAGCAAAAGATTGCT
TCAGAACTGCAGCTTTGGCCACAGGGTGTACAATAGAAATTAAAGCTGGAGCACATGATTATTACAATGTTCTTCCCAAT
AAGACCCTGCGGGAAACTTATATGGAGAATGGAGAAAAA

Alignment

ORF - retro_cpor_790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.01 %
• Parental protein coverage: 76.48 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRPGEERPVQGGACDGVSELEPLELLKLRAAERIDEAAE-RGALSRAIWSEPELAYEEHHAHSLLTRFFQ
          M.PGEERPVQ.GACDGVSELE..E.LKL.AAE..D.A.E..GAL.RAIWSEPELAYEEHHAH.LLTRFF.
Retrocopy MKPGEERPVQCGACDGVSELELQEVLKLCAAEHMD*AVEWLGALTRAIWSEPELAYEEHHAHGLLTRFFE

Parental  QEP-RAASWAVQPHYQLPTAFRA-EWAPGEARAPG-AEVRALQLGFLCE-YDALPGLGHACGHNLIAEVG
          QE...A.S.A.QPH.QLPTAF.A.EWAP..A.APG.A....L.L.FL.E..DALP.....C.HN.IAE..
Retrocopy QES<TATSRALQPHHQLPTAFHAAEWAPPGASAPG<ALKCTLLLAFL*E>KDALPCITYTCSHNFIAEIQ

Parental  AAAALGLRAALESLPGPPPPVKIIVLGTPAEEDGGGKIDLIEAGAFKNLDVVFMAHPSQENAAYLQDVAE
          ..AALGLRAALESLPGPP.PVK.IVLGTPAEEDGGGKIDLIEAGAFKNL.VVFMAH.SQENAA.LQDVAE
Retrocopy TKAALGLRAALESLPGPPQPVKVIVLGTPAEEDGGGKIDLIEAGAFKNLNVVFMAHTSQENAA*LQDVAE

Parental  HDVTVKYYGKASHAAAYPWEGVNALDAAVLAYNNISVLRQQMKPTWRAHGIIKNGGVKP-NIIPSYSELI
          HDVTVK.YGK...AAA.P.EGV.AL.AAVLAYNN.SVLRQQMKPTWR.HGIIKNGG.KP..IIPSYSELI
Retrocopy HDVTVKNYGK---AAA*P*EGVSALNAAVLAYNNVSVLRQQMKPTWRVHGIIKNGG-KP>SIIPSYSELI

Parental  YYFRAPSMKELQVLTKKAEDCFRAAALATGCTIEIKAGAHDYYNVLPNKTLWKTYMENGKK
          .YF.APSMKELQ.L.KKA.DCFR.AALATGCTIEIKAGAHDYYNVLPNKTL..TYMENG.K
Retrocopy CYFHAPSMKELQGLSKKAKDCFRTAALATGCTIEIKAGAHDYYNVLPNKTLRETYMENGEK

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	7.13 RPM
SRP017611_kidney	0.00 RPM	72.76 RPM
SRP017611_liver	0.00 RPM	3.22 RPM
SRP040447_lung	0.00 RPM	5.47 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_790 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_790 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000010921	1 retrocopy	retro_cpor_790 ,
Otolemur garnettii	ENSOGAG00000005200	1 retrocopy	retro_ogar_1012,