RetrogeneDB ID: retro_cpor_490

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:21668152..21669404(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK24
• Ensembl ID: ENSCPOG00000006610
• Aliases: None
• Description: None

Sequence

>retro_cpor_490
CCAGTGCAACCAGGCCAGCCTATCACGCAGAACCTGAAAACAGACCCAAAGGAGCTTTTCACAAAACTGGAGAAGACTGG
AAAGAGCTCTTTTGGTGAGGTGGTCAAAGGCATTGACAGTCAGATTCAGAAGGTGGTTGCCATAAAATTCAGTGATCTGG
AAGAAGCTGAAGATGACACAGAGGACATTCAACAAGAAATCATAATGCTGAGTCAGTGCAATAGTCCATACATAACTAAT
ATTATGAAGGATACAAGTTGTGGATAATAACGGAGTATCTTGGTGATGGCTATGCACTGTATCTATTAGAACCCCACTCT
TTAGATGAAACTCAGATTGCCAGCATATTGAGAGATACTAAAGGGACTCGTTTACCTGCACTCAGAGAAGATCCATAGAG
ATATCAAAGAAGCCAGTGTCCTATTGTCTGAACACCGAAAGGTGAAGCTGGGTGACTTTGGAGTAGATGGACAGCTGACA
GGTACCTAGATAAAGAGGAACACCTTCATGGGCACCCATTTCTGGATGGTGCCTGAGGTCTTCAAAAAGTCAGCATACGA
CTCAAAGGCAGACATCTGTTCCCTGGGTATCACAGCTAGAGAGCAGGCAAGAGGGAAGCCACCCCATTCCAAGCTGCATT
CCATGAAAATTTTATTCCTCATTCCAAAGAACAACCCCCTACACTAGAAGGAAACTACAGCAAGCCCCTCAAGGCGTTTG
TAGAGTCCTGCTTGAATAAGGAGCCGAGCTTTAGACCTACAGCAAAGGGGTTGCTGAAGCACAAGTTTATAATTTGCAAT
CCAAAGAAACGTCCTATCTGATAAAGCTCATCAACAGGTACAAGGAGTGGAAGGCCGAGCAGAGCCACGTGACCCCAGCT
CAGAAGTCTCAGATGCGGAAACAGACAGCCAGGCATCTGAAGGCAGTGGCTCTGGGGACTGGATCTTCACCATCTGAGAG
AAGGACCCAAGAATCTCAAGAATGGAGCTCTTCGGCCCTCGGAGTGGGAAAGAAGTAAGACGAAGACATCCTAAAGAGGC
CTTTCTCTCGGTGTTTATCAACAATTATTTCTCTCTATTCTCAGAGCTGAAGGAGAAGAGTCAATCACGCTGGGAGAACC
TGGAGTCCGTAGACTAGCTGTGTGGCACCGTCTATCTGGCAGCAGAGGCCTGCGGAGCATCTCCAACACCATGGTGACCC
ACTTGTGCAGCAGCTTCAGAGATGTTCTCTAAATAGTGGAGGAACTTCATCC

Alignment

ORF - retro_cpor_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.94 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  PVQPGLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVL
          PVQPG.P..QNLK.DP.ELFTKLEK.GK.SFGEV.KGID...QKVVAIK..DLEEAED..EDIQQEI..L
Retrocopy PVQPGQPITQNLKTDPKELFTKLEKTGKSSFGEVVKGIDSQIQKVVAIKFSDLEEAEDDTEDIQQEIIML

Parental  SQCDSPYVTK-YYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKG-LDYLHSEKKIH
          SQC.SPY.T..YY..Y....KLWII.EYLG.G.AL.LLEP..LDETQIA.ILR...KG.L.YLHSE.KIH
Retrocopy SQCNSPYITN<YYEGY----KLWIITEYLGDGYALYLLEPHSLDETQIASILRD-TKG>LVYLHSE-KIH

Parental  RDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIEL
          RDIK.A.VLLSEH..VKL.DFGV.GQLT.T.IKRNTF.GT.FWM.PEV.K.SAYDSKADI.SLGITA.E.
Retrocopy RDIKEASVLLSEHRKVKLGDFGVDGQLTGT*IKRNTFMGTHFWMVPEVFKKSAYDSKADICSLGITAREQ

Parental  ARGEPPHSELHPMKVLFLIPKNN-PPTLEGSYSKPLKEFVEACLNKEPSFRPTAKELLKHKFIIRNAKK-
          ARG.PPHS.LH.MK.LFLIPKNN.PPTLEG.YSKPLK.FVE.CLNKEPSFRPTAK.LLKHKFII.N.KK.
Retrocopy ARGKPPHSKLHSMKILFLIPKNN<PPTLEGNYSKPLKAFVESCLNKEPSFRPTAKGLLKHKFIICNPKK<

Parental  TSYLTELIDRFKRWKAEQSH-DDSSSEDSDTETDGQASGGNDAGDWIFTIREKD-PKNLENGALQPSELE
          TSYL..LI.R.K.WKAEQSH..D.SSE.SD.ETD.QAS.G...GDWIFTI.EKD.PKNL.NGAL.PSE.E
Retrocopy TSYLIKLINRYKEWKAEQSH<RDPSSEVSDAETDSQASEGSGSGDWIFTI*EKD<PKNLKNGALRPSEWE

Parental  RSKMK-DIPKRPFSQCLSTIIS-PLFAELKEKSQACGGNLGSIEELRGAIYLAEEAC-PGISDTMVAQ-L
          RSK.K.DI.KRPFS.CLSTIIS..LF.ELKEKSQ....NL.S...L.G..YLA.EAC...IS.TMV...L
Retrocopy RSKTK<DILKRPFSRCLSTIIS<SLFSELKEKSQSRWENLESVD*LCGTVYLAAEAC<RSISNTMVTH<L

Parental  VQRLQRYSLSGGGTSS
          VQ.LQR.SL..GGTSS
Retrocopy VQQLQRCSLNSGGTSS

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	30.43 RPM
SRP017611_kidney	0.00 RPM	62.60 RPM
SRP017611_liver	0.00 RPM	14.41 RPM
SRP040447_lung	0.00 RPM	60.58 RPM
SRP040447_skeletal_muscle	0.00 RPM	24.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_490 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_490 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004508	1 retrocopy	retro_cjac_4221,
Cavia porcellus	ENSCPOG00000006610	1 retrocopy	retro_cpor_490 ,
Homo sapiens	ENSG00000102572	1 retrocopy	retro_hsap_4907,
Gorilla gorilla	ENSGGOG00000001983	1 retrocopy	retro_ggor_3065,
Macaca mulatta	ENSMMUG00000009173	1 retrocopy	retro_mmul_2640,
Nomascus leucogenys	ENSNLEG00000007854	1 retrocopy	retro_nleu_2352,