RetrogeneDB ID: retro_cpor_1466

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:5048631..5049863(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000004978
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJA2
• Ensembl ID: ENSCPOG00000006955
• Aliases: None
• Description: Chaperone protein DnaJ [Source:UniProtKB/TrEMBL;Acc:H0V901]

Sequence

>retro_cpor_1466
TCGCAGGCCGCCACGGTGAAGCTGTACGACATCCTGGGTGTCCCGCCCGGCGCCAGCGAGAACGAGCTGAAGAAGGCATA
CAGAAAGTTAGCCAAGGAGTATCATCCTGATAAGAATCCAAATGCTGGAGACAAATTTAAAGAAATAAGTTTTGCATATG
AAGTATTGCCAAATCCAGAGAAGCGCGAGTTATGTGACAGATATGGAGAACAAGGTCTTCGGGAAGGTAGCGGTGGAGGT
GGCGGCATGGATGATATTTTCTCTCACATTTTTGGTGGAGGATTATTTGGCTTTATGGGCAATCAGAGTAGAAGTCGAAA
CGGCAGGAGAAGAGGCGAAGACATGATGCATCCACTCAAAGTATCCTTAGAAGCTCTGTATAATGGCAAAACAACAAACT
ACAAGTTAGCAAGAATGTACTCTGTAGTGCATGCAGTGGTCAAGGTGGAAAATCTGGAGCTGTCCAGAAATGTAGTGCTT
GCCGAGGTCGAGGGGCTCGCGTCATGATCAGACAACTGGCTCCAGGAATGGTGCAACAGATGCAGGCTGTGTGCTCTGAC
TGTAATGGAGAAGGAGAGGTAATTAATGAAAAGGACCGCTGTAAAAAATGTGAAGGGAAGAAGGTGATTAAAGAAGCCAA
GATTCTTGAAGTTCATGTAGACAAAGGCATGAAACATGGACAGAGAATTACATTCACTGGGGAGGCAGACCAGGCCCCAG
GAGTGGAGCCAGGAGACATTGTTCTTTTGCTGCAGGAGAAAGAACATGAGGTGTTCCAGAGAGATGGGAATGATTTGCAC
ATGACTTACAAGATAGGACTTGTTGAAGCTCTGTGTGGATTTCAGTTCACATTTAAGCAGCTTGATGGCCGTCAGATTGT
GCTGAAATACCCTCCTGGCAAAGTAATCGAACCAGGATGTGTTCGTGTAGTCCGAGGTGAAGGAATGCCTCAGTATCGTA
ATCCTTTTGAAAAAGGTGATCTGTACATAAAGTTTGATGTGCAGTTTCCTGAAAACAACTGGATCAACCCAGATAAGCTT
TCTGAGTTAGAAGATCTTCTGCCATCTAGACCAGAGGTTCCTAACATAATTGGAGAAACCGAGGAGGTAGAGCTTCAAGA
GTTTGACAGCACTCGAGGCTCTGGAGGTGGTCAGAGGCGGGAAGCCTATAATGATAGCTCTGATAAAGAGAGCAGCAGCC
ATCACGGGCCTGGGGTGCAGTGTGCCCACCAG

Alignment

ORF - retro_cpor_1466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.87 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ANVADTKLYDILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRYGE
          ...A..KLYDILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVL.NPEKREL.DRYGE
Retrocopy SQAATVKLYDILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLPNPEKRELCDRYGE

Parental  QGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTT-KLQLSKN
          QGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLE.LYNGKTT.KLQ.SKN
Retrocopy QGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLEALYNGKTT<KLQVSKN

Parental  VLCSACSGQGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEGKKV
          VLCSACSGQGGKSGAVQKCSACRGRG.R.MIRQLAPGMVQQMQ.VCSDCNGEGEVINEKDRCKKCEGKKV
Retrocopy VLCSACSGQGGKSGAVQKCSACRGRGARVMIRQLAPGMVQQMQAVCSDCNGEGEVINEKDRCKKCEGKKV

Parental  IKEVKILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEALC
          IKE.KILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEALC
Retrocopy IKEAKILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEALC

Parental  GFQFTFKHLDGRQIVVKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKLSE
          GFQFTFK.LDGRQIV.KYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKLSE
Retrocopy GFQFTFKQLDGRQIVLKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKLSE

Parental  LEDLLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQRREAYNDSSDEESSSHHGPGVQCAHQ
          LEDLLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQRREAYNDSSD.ESSSHHGPGVQCAHQ
Retrocopy LEDLLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQRREAYNDSSDKESSSHHGPGVQCAHQ

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	0.23 RPM	61.89 RPM
SRP017611_kidney	0.10 RPM	59.67 RPM
SRP017611_liver	0.13 RPM	32.04 RPM
SRP040447_lung	0.10 RPM	45.65 RPM
SRP040447_skeletal_muscle	0.13 RPM	56.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1466 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1466 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003757	3 retrocopies	retro_btau_1215, retro_btau_1625, retro_btau_798,
Cavia porcellus	ENSCPOG00000000462	6 retrocopies	retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Cavia porcellus	ENSCPOG00000006955	1 retrocopy	retro_cpor_1466 ,
Dasypus novemcinctus	ENSDNOG00000013794	1 retrocopy	retro_dnov_40,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Oryctolagus cuniculus	ENSOCUG00000004839	1 retrocopy	retro_ocun_1126,
Rattus norvegicus	ENSRNOG00000016251	1 retrocopy	retro_rnor_2778,