RetrogeneDB ID: retro_cpor_1179

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:13010443..13011323(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D4
• Ensembl ID: ENSCPOG00000008945
• Aliases: None
• Description: None

Sequence

>retro_cpor_1179
ATGCACTTGGATGCTGCAGCTGTCAACTTTGAGCTGAACTCTCATCTCTCAGCACTGCAAATCTTCATAAGATCTACCAC
ACCCTTAATAAGCTAAATCTAACCGAGGACATTGGCCAAGAGGATCACCAAACAGGAAGCCTACAGTCTTGCAGGTCTTT
GGGCTGCTTTAGTAAAGTGATACCCAAAGGAAAAAGAGAAGACCTGCCTCTGGAGAGGACTCATCAGGCAAAAAGAGTAG
ACATGATAGCATGTAGAAAATACTGATTCAGTTAGAATGGAGACTGAAGAAGAGGCCTTCTCAAGGAAGCCTAGGCTTAG
GTGGTTCTATGAATATGCAGGTTCATCCTCTACTGAGGATGTTGTAGGTCCCGAAGGAATGGAGAAATTATGTGAAGATG
CTGGTGTAGAATCTGAGGATGTAGTTATGCTTGTCCTAACTTGGAAACCAGATTCACAAAACATGGGTTATTTTACCCTA
CAAGAATGGTTAACAGGAATGACTTCTTTACAACATAATTCAACAGAAAAACTCAGAAATTCTTTGGATTGCTTGAGACC
ACTATTAAATGATTGTACAGACTTTAAGCTTATTTATAGACATGCATTTGACTTTGCACAGGAAAAGGACCAGAGCAGCC
TAGACACAAAGTCTACCAAGTGCATACTGGGACTGTTGTTAGGATAAATCTGGCCCCTTTTTTCCAGTTTTTCATCAATT
CTTAGAGCAATCAAAACATAAAGTGATTAACAAAGACCAGTGGTGCAATGTGCTTGGATTCAGCAAACCAATTAATCTTG
ACCTCAGCAACTGCAATGAAGATGGAGCTCGGCCAGTCTTTTTGGAGGAGTTTGTGGATCAGTATAAAGATAAACAGATG

Alignment

ORF - retro_cpor_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.84 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LHNLALHVDFQLNSHLSTL-ANIHKIYHTLNKLNLTEDVGQDDHQTGSLRSCSSSDCFSKVMPP-RKKRR
          .H..A..V.F.LNSHLS.L.AN.HKIYHTLNKLNLTED.GQ.DHQTGSL.SC.S..CFSKV.P..RKKRR
Retrocopy MHLDAAAVNFELNSHLSAL<ANLHKIYHTLNKLNLTEDIGQEDHQTGSLQSCRSLGCFSKVIPK<RKKRR

Parental  PASGDDLSAKKSRHDSM-YRKYDSTRIKTEEEAFSSKRCLEWFYEYAG---TEDVVGPEGMEKFCEDIGV
          PASG.D.S.KKSRHDSM.....DS.R..TEEEAFS.K..L.WFYEYAG...TEDVVGPEGMEK.CED.GV
Retrocopy PASGEDSSGKKSRHDSM<VENTDSVRMETEEEAFSRKPRLRWFYEYAGSSSTEDVVGPEGMEKLCEDAGV

Parental  EPENVVMLVLAWKLDAQNMGYFTLQEWLTGMTSLQCDTTEKLRNSLDCLRSLLNDSTNFKLIYRYAFDFA
          E.E.VVMLVL.WK.D.QNMGYFTLQEWLTGMTSLQ...TEKLRNSLDCLR.LLND.T.FKLIYR.AFDFA
Retrocopy ESEDVVMLVLTWKPDSQNMGYFTLQEWLTGMTSLQHNSTEKLRNSLDCLRPLLNDCTDFKLIYRHAFDFA

Parental  REKDQRSLDINTAKCMLGLLLGKIWPL-FPVFHQFLEQSKYKVINKDQWCNVLEFSRTIHLDLSNYDEDG
          .EKDQ.SLD....KC.LGLLLG.IWPL.FPVFHQFLEQSK.KVINKDQWCNVL.FS..I.LDLSN..EDG
Retrocopy QEKDQSSLDTKSTKCILGLLLG*IWPL>FPVFHQFLEQSKHKVINKDQWCNVLGFSKPINLDLSNCNEDG

Parental  AWPVLLDEFVEWYKDKQM
          A.PV.L.EFV..YKDKQM
Retrocopy ARPVFLEEFVDQYKDKQM

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	20.36 RPM
SRP017611_kidney	0.00 RPM	16.23 RPM
SRP017611_liver	0.00 RPM	13.10 RPM
SRP040447_lung	0.00 RPM	12.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.19 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1179 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1179 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018601	1 retrocopy	retro_cjac_3959,
Cavia porcellus	ENSCPOG00000008945	2 retrocopies	retro_cpor_1176, retro_cpor_1179 ,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Sarcophilus harrisii	ENSSHAG00000017879	1 retrocopy	retro_shar_437,