RetrogeneDB ID: retro_rnor_2009

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:212385363..212386148(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046495
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nudc
• Ensembl ID: ENSRNOG00000007399
• Aliases: Nudc, Silg92, c15
• Description: Nuclear migration protein nudC [Source:UniProtKB/Swiss-Prot;Acc:Q63525]

Sequence

>retro_rnor_2009
ATGGGAGGGGAGCAGGAGGAAGAGCTCTTCGACAGCATGCTGCTGGCCATGGCGCAGCAGCACGAAGGCAGCATGCAGGA
GCTTGTGAACAACTTCTTCAGCTCCTTCAACGCAAAACAGACTTTTTCATTGGAGGAGAAGAGGGGATGGCAGAGAAGCT
CGTCACACAGACTTTTAACCACCACAACCAGCTGGCACAGAAGGCCAGAAGACAGAAGCGAGCTCGGCAGGAGACTGAGC
GTCGGGAGAAGGCAGAACAGGCAGCCAGACTGGCCAAGGATGCCAAGGCAGAGACTCCCGGGTCACAGATCAAGGAACTG
ACTGATGAGGAGGAGGAGAGACTGCAGGTGGAGATTGACCAGAAAAAGGATGCAGAGCATCATGAGGTGCAGCTCAAGAA
TGGCAGTCTTGACTCACCAGGGAAGCAGGAGGCCGAGGAGGAGGAAGACGAGAAGGACAAAGGAAAACTGAAACCCAACG
TAGGCAATGGGGCTGACTTGCCCAACTACCGCTGGACCCAGACCCTGTCAGAGCTGGATCTGGCAGTGCCCTTCCAAGTC
AGCTTCCGACTGAAGGGAAAGAATGTGGTGGTGGACATCCAGCGGCGGCACCTCCAGGTGGGCCTCAAAGGACAGGCACC
AGTGACTGATGGAGAACTCTACAATGAAGTAAAGGTGGAGGAGAGCTCGTGGCACATCGAAGATGGCAAGGTGGTGACAG
TTCATCTGGAGAAGATCAATAAGATGGAATGGTGGAACCGCTTGGTTACCAGTGACCCCGAAATC

Alignment

ORF - retro_rnor_2009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 79.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGEQEEERFDGMLLAMAQQHEGGVQELVNTFFS-FLRRKTDFFIGGEEGMAEKLITQTFNHHNQLAQKA
          MGGEQEEE.FD.MLLAMAQQHEG..QELVN.FFS..L.RKTDFFIGGEEGMAEKL.TQTFNHHNQLAQKA
Retrocopy MGGEQEEELFDSMLLAMAQQHEGSMQELVNNFFS<LLQRKTDFFIGGEEGMAEKLVTQTFNHHNQLAQKA

Parental  RREKRARQETERREKAERAARLAKEAKAETPGPQIKELTDEEAERLQLEIDQKKDAENHEVQLKNGSLDS
          RR.KRARQETERREKAE.AARLAK.AKAETPG.QIKELTDEE.ERLQ.EIDQKKDAE.HEVQLKNGSLDS
Retrocopy RRQKRARQETERREKAEQAARLAKDAKAETPGSQIKELTDEEEERLQVEIDQKKDAEHHEVQLKNGSLDS

Parental  PGKQDAEEEEDEEDEKDKGKLKPNLGNGADLPNYRWTQTLSELDLAVPFRVSFRLKGKDVVVDIQRRHLR
          PGKQ.AEE...EEDEKDKGKLKPN.GNGADLPNYRWTQTLSELDLAVPF.VSFRLKGK.VVVDIQRRHL.
Retrocopy PGKQEAEE---EEDEKDKGKLKPNVGNGADLPNYRWTQTLSELDLAVPFQVSFRLKGKNVVVDIQRRHLQ

Parental  VGLKGQAPVIDGELYNEVKVEESSWLIEDGKVVTVHLEKINKMEWWNRLVTSDPEI
          VGLKGQAPV.DGELYNEVKVEESSW.IEDGKVVTVHLEKINKMEWWNRLVTSDPEI
Retrocopy VGLKGQAPVTDGELYNEVKVEESSWHIEDGKVVTVHLEKINKMEWWNRLVTSDPEI

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	7.48 RPM
SRP017611_kidney	0.00 RPM	4.75 RPM
SRP017611_liver	0.00 RPM	3.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2009 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2009 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001291	1 retrocopy	retro_eeur_526,
Homo sapiens	ENSG00000090273	2 retrocopies	retro_hsap_2168, retro_hsap_2183,
Gorilla gorilla	ENSGGOG00000015314	2 retrocopies	retro_ggor_1720, retro_ggor_1730,
Microcebus murinus	ENSMICG00000015671	1 retrocopy	retro_mmur_457,
Mus musculus	ENSMUSG00000028851	1 retrocopy	retro_mmus_3181,
Nomascus leucogenys	ENSNLEG00000009404	2 retrocopies	retro_nleu_2545, retro_nleu_312,
Pongo abelii	ENSPPYG00000001673	2 retrocopies	retro_pabe_2055, retro_pabe_2064,
Pan troglodytes	ENSPTRG00000000395	2 retrocopies	retro_ptro_1655, retro_ptro_1661,
Pteropus vampyrus	ENSPVAG00000004408	1 retrocopy	retro_pvam_434,
Rattus norvegicus	ENSRNOG00000007399	2 retrocopies	retro_rnor_2009 , retro_rnor_2108,