RetrogeneDB ID: retro_rnor_994

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:10571468..10572329(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000002200
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nrbf2
• Ensembl ID: ENSRNOG00000000641
• Aliases: None
• Description: nuclear receptor-binding factor 2 [Source:RefSeq peptide;Acc:NP_071522]

Sequence

>retro_rnor_994
ATGGAAGTGATGGAAGGACCCCTCAACCTTGCTCACCAACAGAGCCGACGGGCAGACCGTTTGTTAGCTGCTGGGAAATA
CGAAGAAGCGATTTCTTGTCACAAAAAGGCGACAGCCTATCTCTCTGAAGCCATGAAGCTGACACAGTCTGAGCAGGCTC
ACTTATCACTGGAACTGCAAAGGGATAGCCACATGAAGCAGCTTCTCCTCATCCAGGAGAGGTGGAAGAGAGCGAAGCGA
GAGGAGCGGTTGAAAGCGCAGCAGAGCACAGACCGGGATGGAGTCCCCCACCTGCAGGCATCTCACAGACCCTCTGAGGA
CTCGGAAGGCCAGAGCCCTCTTCTTTCTCAGACAGACATCCCTTCCACAGAGAAGCGCCTCCCTGAGGTGCAGGGGGTCT
TTGACAGGGATCCAGACACGTTGCTATTTTTACTTCAGCAAAAGAATGAGCCGTCAGAGCCCTGTATTGGAAGCAAGGCC
CCAAAAGATGATAAGACGATTATAGAGGAGCAGGCAACCAAGATTGCAGAGTTGAAGAGGCACGTGGAGTTCCTTGTGGC
GGAGAACGAAAGACTAAGGAAAGAAAATAAACAGCTAAAGGCTGAAAAGGCCAGGCTCCTGAAGGGCCCAGCCGAGAAGG
AGCTGGACGTCGATGCGGACTTTGTGGAGAAGTCGGAGCTGTGGGGCTTGCCGCCACACTCGGACACCGCCACTGCCTCT
TCTACCTGGCAGAAGTTTGCAGCTAACACCGGGAAAGCCAAGGACATTCCAATACCCAACCTCCGGCCTCTGGATTTCCC
GTCTCCAGAACTCCCTCTGATGGAGCTCTCGGAGGACATTCTGAAAGGATTCATGAATGAC

Alignment

ORF - retro_rnor_994 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKATAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
          MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKATAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
Retrocopy MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKATAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL

Parental  IQERWKRAKREERLKAQQSTDRDGVPHLQASHRPSEDSEGQSPLLSQTYIPSTEKRLPEVQGVFDRDPDT
          IQERWKRAKREERLKAQQSTDRDGVPHLQASHRPSEDSEGQSPLLSQT.IPSTEKRLPEVQGVFDRDPDT
Retrocopy IQERWKRAKREERLKAQQSTDRDGVPHLQASHRPSEDSEGQSPLLSQTDIPSTEKRLPEVQGVFDRDPDT

Parental  LLFLLQQKNEPSEPCIGSKAPKDDKTIIEEQATKIAELKRHVEFLVAENERLRKENKQLKAEKARLLKGP
          LLFLLQQKNEPSEPCIGSKAPKDDKTIIEEQATKIAELKRHVEFLVAENERLRKENKQLKAEKARLLKGP
Retrocopy LLFLLQQKNEPSEPCIGSKAPKDDKTIIEEQATKIAELKRHVEFLVAENERLRKENKQLKAEKARLLKGP

Parental  AEKELDVDADFVEKSELWGLPPHSDTATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI
          AEKELDVDADFVEKSELWGLPPHSDTATASSTWQKFAANTGKAKDIPIPNL.PLDFPSPELPLMELSEDI
Retrocopy AEKELDVDADFVEKSELWGLPPHSDTATASSTWQKFAANTGKAKDIPIPNLRPLDFPSPELPLMELSEDI

Parental  LKGFMND
          LKGFMND
Retrocopy LKGFMND

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	4.17 RPM
SRP017611_kidney	0.00 RPM	3.84 RPM
SRP017611_liver	0.00 RPM	10.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_994 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_994 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994 ,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183,