RetrogeneDB ID: retro_cpor_876

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_30:5161548..5162090(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDE1
• Ensembl ID: ENSCPOG00000019614
• Aliases: None
• Description: None

Sequence

>retro_cpor_876
CAAATGGAAACCAGAAACCAAGACCTCATGTCAGAGAGTAATAGCCTTTTCATGGAGCTGGAAACTGTCAGGCAAAACTT
TGAAATGCAGCATTTTGAAGGCTACAGAAAGATTTCAGCTTTGGAAGATGACCTGACACAAATGAAAGCAATTAAAGATC
AACTGCTGAATACATCAGGGAGCTGGAGAAAGCAAACAGTTGCTTGGAAAGAGCCAAACAAGCCATGATCATGTCTCTGG
AAGACTTTGAGCAGCACTTGAATCAAGACATTGAAAGAAACGAATTCCTGGAAAGTGAATTTGATGAGAAGCAGAATCTC
CTACAATCTGTTCAGTGTCTAAAGGATGAAGCCAAAGATTTGATGCAGGAATTGGCTGTACAATAGAAGCAAGAGAAGTC
CAGAACACCCATACCCAGTACAGTGGAAGCCAAACCCACAGACATAAATCTGCAGGCCACGGGATCCGTACTGTACACTT
ATATCACTCATCAATGACTTGGGTCTGGTTTAAACACCCCATGGGCATTTAGTCACCAACAG

Alignment

ORF - retro_cpor_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.74 %
• Parental protein coverage: 51.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QIETRNRDLLSENNRLRMELETVKEKFEMQHSEGYRQISALEDDLAQTKAIKDQL-QKYIRELEQANDDL
          Q.ETRN.DL.SE.N.L.MELETV...FEMQH.EGYR.ISALEDDL.Q.KAIKDQL...YIRELE.AN..L
Retrocopy QMETRNQDLMSESNSLFMELETVRQNFEMQHFEGYRKISALEDDLTQMKAIKDQL<AEYIRELEKANSCL

Parental  ERAKRATIMSLEDFEQRLNQAIERNAFLESELDEKENLLESVQRLKDEARGTDLRQELAVQQKQEKPRTP
          ERAK.A.IMSLEDFEQ.LNQ.IERN.FLESE.DEK.NLL.SVQ.LKDEA...DL.QELAVQ.KQEK.RTP
Retrocopy ERAKQAMIMSLEDFEQHLNQDIERNEFLESEFDEKQNLLQSVQCLKDEAK--DLMQELAVQ*KQEKSRTP

Parental  MPSAVEAERTDIAVQATGSVPSTPIAHRGLGSALNTPGTFRRAQ
          .PS.VEA..TDI..QATGSV..T.I.H..LGS.LNTP..F...Q
Retrocopy IPSTVEAKPTDINLQATGSVLYTYITHQ*LGSGLNTPWAFSHQQ

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	22.72 RPM
SRP017611_kidney	0.00 RPM	13.50 RPM
SRP017611_liver	0.00 RPM	8.84 RPM
SRP040447_lung	0.00 RPM	43.38 RPM
SRP040447_skeletal_muscle	0.00 RPM	16.23 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_876 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_876 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009557	1 retrocopy	retro_amel_104,
Canis familiaris	ENSCAFG00000018722	1 retrocopy	retro_cfam_1579,
Choloepus hoffmanni	ENSCHOG00000006004	1 retrocopy	retro_chof_1270,
Cavia porcellus	ENSCPOG00000012878	1 retrocopy	retro_cpor_626,
Cavia porcellus	ENSCPOG00000019614	2 retrocopies	retro_cpor_875, retro_cpor_876 ,
Ictidomys tridecemlineatus	ENSSTOG00000019896	1 retrocopy	retro_itri_1101,
Tupaia belangeri	ENSTBEG00000005260	1 retrocopy	retro_tbel_1468,