RetrogeneDB ID: retro_rnor_2686

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:52603580..52604030(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Plp2
• Ensembl ID: ENSRNOG00000039496
• Aliases: Plp2, A4-LSB
• Description: Proteolipid protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q6P742]

Sequence

>retro_rnor_2686
ATGGCGGACTCTGAGCGTCTCTCGGCTCCCGGCTGCTGGTTAGCCTGCACCAGCTTCTCGCGCAGCAAAAAGGGAATTCT
CCTGTTTGCTGAGATTATACTGTGCCTGGTGATTTTGATTTGCTTCAGTGCGTCTACATCGGCCTACTCCTCCCTGTTGG
CGATTGAGATGATCTTTGTTGCTGTCTTATTTGTCTTCTACGTGTGTCACCTGCACTCCAAGATATCATTCATCAGTTGG
CCTTGGACCGATTTCTTCAGATCCCTCATAGCCATCCTGTACCTGATCACTTCCATTGTTGTCCTTGTAGAAGGAAGAGG
CAGCTCCATATTCGTCGCTGGGGTGCTGGGCTTGTTGGCTACATTGCTCTTTGGTTATGATGCATACATCACCTTCCCTC
TAAAGCAGCAAAGACATACAGCATCTCCTACTGACCCCACAAATGGCCCA

Alignment

ORF - retro_rnor_2686 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADSERLSAPGCWLACTSFSRTKKGILLFAEIILCLVILICFSASTSAYSSLSVIEMIFAAVLFVFYMCD
          MADSERLSAPGCWLACTSFSR.KKGILLFAEIILCLVILICFSASTSAYSSL..IEMIF.AVLFVFY.C.
Retrocopy MADSERLSAPGCWLACTSFSRSKKGILLFAEIILCLVILICFSASTSAYSSLLAIEMIFVAVLFVFYVCH

Parental  LHSKISFINWPWTDFFRSLIAAILYLITSIVVLVEGRGSSKIVAGVLGLLATLLFGYDAYITFPLKQQRH
          LHSKISFI.WPWTDFFRSLI.AILYLITSIVVLVEGRGSS..VAGVLGLLATLLFGYDAYITFPLKQQRH
Retrocopy LHSKISFISWPWTDFFRSLI-AILYLITSIVVLVEGRGSSIFVAGVLGLLATLLFGYDAYITFPLKQQRH

Parental  TAAPTDPTDGP
          TA.PTDPT.GP
Retrocopy TASPTDPTNGP

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	1.22 RPM
SRP017611_kidney	0.00 RPM	12.28 RPM
SRP017611_liver	0.00 RPM	2.42 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2686 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2686 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2686 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810,
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Rattus norvegicus	ENSRNOG00000039496	1 retrocopy	retro_rnor_2686 ,