RetrogeneDB ID: retro_rnor_2336

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:149904143..149905058(+)
• Located in intron of: ENSRNOG00000045938

Retrocopy information

• Ensembl ID: ENSRNOG00000006321
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpf2
• Ensembl ID: ENSRNOG00000000587
• Aliases: Rpf2, Bxdc1
• Description: ribosome production factor 2 homolog [Source:RefSeq peptide;Acc:NP_001099861]

Sequence

>retro_rnor_2336
ATGGATGCTTTGGACAAAGTCCTAAAGCCTAAAACAAAAAGGGCTAAGAGATTCCTTGAGAAGATGGAGTCAAAACTCAG
TGAAAATATTAAGAATGCCATGATGATTAAAGATGGGAGTGTGAATGCAAGGGTGACACAAGTACTCAGAGACATGTATG
CCCGGAAGAAACCATATGGAGTTCTCTATAAAAATAAAAATATTACAAGACCATTTGAGGATCAGACCTCACTGGAGTTC
TTTTTAAAGAAGTCAGACTCTTCTCTATTCATGTTTCGCTCCCATAATAAGAAGAGGCCCAATAATCTAGTAATAGGTCG
TATGTATGACTACCATGTGCTGGATATGATTGAACTAGGGATTGAGAAATTTGTGTCTCTGAAAGATACTAACACAAGTA
AGTGCCCCGAGGGAACAAAGCCCATGTTGATATTTGCTGGTAATGATTTTGATGTAAAAGAAGACCACAGAAATATAAAA
AATCTTATTGATTTCTTCAGAGGCCCCACAGTGTCAAACGTCCGTCTGTCTGGATTAGAGTATGTTCTGCACTTCATGGC
ACTGAATGGGAAGGTTTACTTTCGAAGCTGCAAGCTGCTGCTGAAGAAAACTGGGTGCAGAAGACCCCGAATCGACCTAG
AAGAGATGGGGCCGTCTTTGGAGCTGGTTGTGAGGAGGACACACTTAGCATCAGACAAACTTTATAAGCTGTCCATGAAA
GTGCCCAAAGCTCTCAAGCCTAAGAAGAGGAAGAATATCTCTCAGGATACTTTTGGTACAACGTTTGGAAGGATTCATAT
GCAGAAGCAAGACCTAAGCAAACTACAGACAAGGAAAGTGAAGGGGTTAAAGAAGCGGCCTGCAGAGAATGGGATAGAAG
ACTAGGGGAAGAAATTAAAGAGAATTAAGAAAAAT

Alignment

ORF - retro_rnor_2336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDALDKVLKPKTKRAKRFLEKREPKLSENIKNAMLIKGGNANATVTQVLRDVYALKKPYGVLYKKKNITR
          MDALDKVLKPKTKRAKRFLEK.E.KLSENIKNAM.IK.G..NA.VTQVLRD.YA.KKPYGVLYK.KNITR
Retrocopy MDALDKVLKPKTKRAKRFLEKMESKLSENIKNAMMIKDGSVNARVTQVLRDMYARKKPYGVLYKNKNITR

Parental  PFEDQTSLEFFSKKSDCSLFMFGSHNKKRPNNLVIGRMYDYHVLDMIELGIEKFVSLKDIKTSKCPEGTK
          PFEDQTSLEFF.KKSD.SLFMF.SHNKKRPNNLVIGRMYDYHVLDMIELGIEKFVSLKD..TSKCPEGTK
Retrocopy PFEDQTSLEFFLKKSDSSLFMFRSHNKKRPNNLVIGRMYDYHVLDMIELGIEKFVSLKDTNTSKCPEGTK

Parental  PMLIFAGDDFDVTEDYRRLKNLLIDFFRGPTVSNVRLAGLEYVLHFTALNGKVYFRSYKLLLKKSGCRTP
          PMLIFAG.DFDV.ED.R..KN.LIDFFRGPTVSNVRL.GLEYVLHF.ALNGKVYFRS.KLLLKK.GCR.P
Retrocopy PMLIFAGNDFDVKEDHRNIKN-LIDFFRGPTVSNVRLSGLEYVLHFMALNGKVYFRSCKLLLKKTGCRRP

Parental  RIELEEMGPSLDLVVRRTHLASDDLYKLSMKVPKALKPKKRKNISQDTFGTTFGRIHMQKQDLSKLQTRK
          RI.LEEMGPSL.LVVRRTHLASD.LYKLSMKVPKALKPKKRKNISQDTFGTTFGRIHMQKQDLSKLQTRK
Retrocopy RIDLEEMGPSLELVVRRTHLASDKLYKLSMKVPKALKPKKRKNISQDTFGTTFGRIHMQKQDLSKLQTRK

Parental  VKGLKKRPAENGVEDQGKKSKRIKKS
          VKGLKKRPAENG.ED.GKK.KRIKK.
Retrocopy VKGLKKRPAENGIED*GKKLKRIKKN

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	15.53 RPM
SRP017611_kidney	0.00 RPM	5.79 RPM
SRP017611_liver	0.00 RPM	4.91 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2336 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2336 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003918	2 retrocopies	retro_cfam_1611, retro_cfam_903,
Callithrix jacchus	ENSCJAG00000005212	6 retrocopies	retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473, retro_cjac_606, retro_cjac_933,
Cavia porcellus	ENSCPOG00000006797	2 retrocopies	retro_cpor_332, retro_cpor_582,
Equus caballus	ENSECAG00000017121	1 retrocopy	retro_ecab_782,
Erinaceus europaeus	ENSEEUG00000006169	2 retrocopies	retro_eeur_454, retro_eeur_584,
Felis catus	ENSFCAG00000001527	1 retrocopy	retro_fcat_1584,
Homo sapiens	ENSG00000197498	1 retrocopy	retro_hsap_2425,
Gorilla gorilla	ENSGGOG00000001469	1 retrocopy	retro_ggor_83,
Myotis lucifugus	ENSMLUG00000005676	2 retrocopies	retro_mluc_485, retro_mluc_921,
Macaca mulatta	ENSMMUG00000021532	1 retrocopy	retro_mmul_1903,
Mus musculus	ENSMUSG00000038510	1 retrocopy	retro_mmus_2234,
Nomascus leucogenys	ENSNLEG00000012854	3 retrocopies	retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus	ENSOCUG00000016028	1 retrocopy	retro_ocun_831,
Pongo abelii	ENSPPYG00000016925	2 retrocopies	retro_pabe_1788, retro_pabe_2464,
Pan troglodytes	ENSPTRG00000018503	1 retrocopy	retro_ptro_1398,
Rattus norvegicus	ENSRNOG00000000587	1 retrocopy	retro_rnor_2336 ,
Tupaia belangeri	ENSTBEG00000017151	9 retrocopies	retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,