RetrogeneDB ID: retro_cpor_740

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:10652189..10652609(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5S
• Ensembl ID: ENSCPOG00000014471
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B) [Source:HGNC Symbol;Acc:18799]

Sequence

>retro_cpor_740
TCCCTACATTACTGTGGCCAGGAGAGGTGGCAGAAAGGCTCCAACTACCTCCCAACAGGCCCCTTGGACAAATCCAAGAT
TCAAGCAATCAATGAAACAGAATTTTGCATCAATAACATTGGATTAGATCACATGAATCGTCTACAACATGTTGAAAAAA
TAAAATTATACAAGTGCAACTATATTGAGGATGAGTGCTTGGTAAGAATTCATCAACATGAATATTTGCAGAAAAGCATA
TTGGAAATAAAAATAATTTCCTATAGGAATGTCACAGATAAGGGCACCATTGCTTTGCATCATTTAAGAAACCTCAAGTA
TTTGTTGTTAAGTGATCTTGCTGGAGTAAGAGAAAAAAAAAAGATTGTCCAAGTTTTTAAGACAATACTATCTTAGCTTG
AACTAAAATTAAAATTGAAG

Alignment

ORF - retro_cpor_740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 70. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVRYHGQERWQKDYNQLPTGPLDKYKIQAIDATDSCIMNIGFDHMEGLEHVEKIKLCKCHYIEDDCLLRI
          ...Y.GQERWQK..N.LPTGPLDK.KIQAI..T..CI.NIG.DHM..L.HVEKIKL.KC.YIED.CL.RI
Retrocopy SLHYCGQERWQKGSNYLPTGPLDKSKIQAINETEFCINNIGLDHMNRLQHVEKIKLYKCNYIEDECLVRI

Parental  SQLEKLQKSLLEMEIISCGNVTDKGIVALRHLRNLKYLLLSDLPGVREKENIVQVFKTTLPSLELELQLK
          .Q.E.LQKS.LE..IIS..NVTDKG..AL.HLRNLKYLLLSDL.GVR....IVQVFKT.L..LEL.L.LK
Retrocopy HQHEYLQKSILEIKIISYRNVTDKGTIALHHLRNLKYLLLSDLAGVRXXXXIVQVFKTILS*LELKLKLK

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	5.87 RPM
SRP017611_kidney	0.00 RPM	7.22 RPM
SRP017611_liver	0.00 RPM	8.01 RPM
SRP040447_lung	0.00 RPM	3.25 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.93 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_740 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_740 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009828	1 retrocopy	retro_amel_377,
Canis familiaris	ENSCAFG00000014285	1 retrocopy	retro_cfam_267,
Cavia porcellus	ENSCPOG00000014471	1 retrocopy	retro_cpor_740 ,
Felis catus	ENSFCAG00000029962	1 retrocopy	retro_fcat_72,
Loxodonta africana	ENSLAFG00000013773	1 retrocopy	retro_lafr_167,
Pteropus vampyrus	ENSPVAG00000006173	1 retrocopy	retro_pvam_539,
Sorex araneus	ENSSARG00000007707	1 retrocopy	retro_sara_694,