RetrogeneDB ID: retro_rnor_820

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:2242511..2242940(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gmnn
• Ensembl ID: ENSRNOG00000018782
• Aliases: None
• Description: geminin [Source:RefSeq peptide;Acc:NP_001099582]

Sequence

>retro_rnor_820
CTGAATCCTTGTATGAAGCAGAACGAGGAAGGGGCCCAAGGGAAGGTGAAGAACAGTTCTGTTCCAAGGAGCATGCTGAA
GATGATTCGGCCTCCTGTAGCTGGGTCTCTTGCTGGCAGACAGAACGAGTTGCCAAAAGGCTTGTCCAAAAGAAAGCTTT
AGGATGACCAGCTAACATCTGAGACTTTGAGCTGTGGTCCAGAAGCTAATGAAAATAGATGCAGAAGCATCATTCAGGAA
GCATTTGATCTTATGATTAAAGAAAACCCATCTTCTCAGTATTGGAGAGAAGTAGTAGAAAAACAGAGCAACGCTCTAGA
TGAAGCACTTAAAGAGAGGGGGAAACTTCATAAAGAAATTGAACAAAGGGGCAGTGGAATCACCTGTCTGAAAAGGGAGA
ATGAAGGCGTAGCAGAAGTATCAGAACAC

Alignment

ORF - retro_rnor_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.28 %
• Parental protein coverage: 69.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLSMKQKQEGAQENVKSSPVPRRTLKMIQPSAAGSLVGRENELPKGLSKRKLWDDQLTSKISSCGPEAN
          .N..MKQ..EGAQ..VK.S.VPR..LKMI.P..AGSL.GR.NELPKGLSKRKL.DDQLTS...SCGPEAN
Retrocopy LNPCMKQNEEGAQGKVKNSSVPRSMLKMIRPPVAGSLAGRQNELPKGLSKRKL*DDQLTSETLSCGPEAN

Parental  ENNSVGDLTQEACDLMTKENPSSQYWKEVAEQRRKALYEALTENEKLHKEIEQKDSEIARLRKENKDLAE
          EN.......QEA.DLM.KENPSSQYW.EV.E....AL.EAL.E..KLHKEIEQ..S.I..L..EN...AE
Retrocopy ENR-CRSIIQEAFDLMIKENPSSQYWREVVEKQSNALDEALKERGKLHKEIEQRGSGITCLKRENEGVAE

Parental  VAEH
          V.EH
Retrocopy VSEH

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	2.08 RPM
SRP017611_kidney	0.00 RPM	1.12 RPM
SRP017611_liver	0.00 RPM	1.21 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_820 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_820 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006161	1 retrocopy	retro_cjac_1012,
Microcebus murinus	ENSMICG00000014010	1 retrocopy	retro_mmur_594,
Myotis lucifugus	ENSMLUG00000014849	2 retrocopies	retro_mluc_1589, retro_mluc_743,
Monodelphis domestica	ENSMODG00000011682	1 retrocopy	retro_mdom_1800,
Mus musculus	ENSMUSG00000006715	2 retrocopies	retro_mmus_1525, retro_mmus_2213,
Oryctolagus cuniculus	ENSOCUG00000000728	1 retrocopy	retro_ocun_613,
Otolemur garnettii	ENSOGAG00000004982	1 retrocopy	retro_ogar_1726,
Ochotona princeps	ENSOPRG00000007969	1 retrocopy	retro_opri_439,
Rattus norvegicus	ENSRNOG00000018782	1 retrocopy	retro_rnor_820 ,
Sarcophilus harrisii	ENSSHAG00000004058	2 retrocopies	retro_shar_581, retro_shar_769,
Tupaia belangeri	ENSTBEG00000010502	2 retrocopies	retro_tbel_1028, retro_tbel_353,