RetrogeneDB ID: retro_cpor_626

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:6637306..6637902(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDEL1
• Ensembl ID: ENSCPOG00000012878
• Aliases: None
• Description: None

Sequence

>retro_cpor_626
CTGCATAAGCATGTGAGAGAGCTGGAGCCGGCCAATGATGACCTGGGACGAGGAGCAAAAAAAGCAACAGCACTTTCACT
GGAAGACTTGGAACAAAGGCTAAGTCAGGCCACTGAATGAAATACACTTGTTGAAAGTAAACTTGATGAAAAGAAATTTC
TGTTGGATTCTGTACAGAGGTAAAAGGATGCAGCAAGAGATTTAAGGCAAGAATTAGCAGTGCAGGAAAAACAGCAAATG
ACCCGAAAGTCGGCTCCCAGTGCTCCAACTGTGGACTTTGAGAAGAGGGATTCTGCTGTGCAGGCTTTGCTCTCCTTGCT
GGCTATCCCTGTTGCCAAAGCAACAGAAAACAGCTTTTCCCTAAAAGCTGTACCAAATAATTTTGGAACCAGTCCCTTAA
CTCCTTCAGGTAGGATATCAGCACTAAACATTGTGGGGGATCCCTTACGGAAAGTAGGGGCTTCAGAATCCAAGTTAGCA
GCTTGTAGGAACTTTGCAAAGGACCAGGCAGCAGGAAAATTTTATATTTCAGAGAATATTAACCATGGAGTCATGACCAG
CAATGGCAAAAGTTCTCTCAATCAAGGCACAGTACT

Alignment

ORF - retro_cpor_626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 57.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LHKYVRELEQANDDLER-AKRATIVSLEDFEQRLNQAIERNAFLESELDEKESLLVSVQRLKDEARDLRQ
          LHK.VRELE.ANDDL.R.AK.AT..SLED.EQRL.QA.E.N...ES.LDEK..LL.SVQR.KD.ARDLRQ
Retrocopy LHKHVRELEPANDDLGRGAKKATALSLEDLEQRLSQATE*NTLVESKLDEKKFLLDSVQR*KDAARDLRQ

Parental  ELAVRERQQEVTRKSAPSSPTLDCEKMDSAVQASLSLPATPVGKGTENSFPSPKAIPNGFGTSPLTPSAR
          ELAV.E.QQ..TRKSAPS.PT.D.EK.DSAVQA.LSL.A.PV.K.TENSF.S.KA.PN.FGTSPLTPS.R
Retrocopy ELAVQEKQQ-MTRKSAPSAPTVDFEKRDSAVQALLSLLAIPVAKATENSF-SLKAVPNNFGTSPLTPSGR

Parental  ISALNIVGDLLRKVGALESKLAACRNFAKDQAARKSYISGNVNCGVMNSNG-TKFSRSGHTS
          ISALNIVGD.LRKVGA.ESKLAACRNFAKDQAA.K.YIS.N.N.GVM.SNG..KFS.S.H..
Retrocopy ISALNIVGDPLRKVGASESKLAACRNFAKDQAAGKFYISENINHGVMTSNG<QKFSQSRHST

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	38.71 RPM
SRP017611_kidney	0.00 RPM	19.68 RPM
SRP017611_liver	0.00 RPM	7.09 RPM
SRP040447_lung	0.00 RPM	19.55 RPM
SRP040447_skeletal_muscle	0.00 RPM	15.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_626 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_626 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014341	1 retrocopy	retro_cjac_4072,
Cavia porcellus	ENSCPOG00000012878	1 retrocopy	retro_cpor_626 ,
Cavia porcellus	ENSCPOG00000019614	2 retrocopies	retro_cpor_875, retro_cpor_876,
Pan troglodytes	ENSPTRG00000008744	1 retrocopy	retro_ptro_2000,
Ictidomys tridecemlineatus	ENSSTOG00000027930	1 retrocopy	retro_itri_620,
Tursiops truncatus	ENSTTRG00000006517	1 retrocopy	retro_ttru_1239,