RetrogeneDB ID: retro_rnor_1828

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:137742915..137743340(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rbm8a
• Ensembl ID: ENSRNOG00000021215
• Aliases: Rbm8a, Rbm8
• Description: RNA-binding protein 8A [Source:UniProtKB/Swiss-Prot;Acc:Q27W01]

Sequence

>retro_rnor_1828
GACGAAAGCATCCACAAACTAGGAGAAAAAGCAAAGAAACTGAAGGGCCTCAGTTTTGGCTCTGAGGGATCCCAAGCATG
AACGTGGGAGGATTATGACAGTTTGGAGCAGGATGTCGATGAGCCTGGACCACAGCACTCTGTTGAAGTTTAGATTCTCT
TTGTCACTGGAGTCCACGAAGAAGCCACTGAAGAAGATATCCATGACAAACTCTCTGAATATGGATAAATAATAAATATC
CATCTTAATTTGGACAGGCACACAGGATGTTTGAAGGAGTATACTCTAGCTGAGTATGAAACATACAAAGAGGATCAGGC
TGCCATCGAGGGACTAAATGGACAAGATTTGATGGGACAGCCAATCAGTATTCACTGGTGTTTTGTTTGTGGTTCACCAA
AGGGCGAAGAAGACGAAGCAGGAGA

Alignment

ORF - retro_rnor_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 82.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHD
          DESIHKL.EKAKK.KG..FGSE.GS.A...EDYDS.EQD.DEPGPQ.SVE..ILFVTGVHEEATEEDIHD
Retrocopy DESIHKLGEKAKKLKGLSFGSE-GSQA*TWEDYDSLEQDVDEPGPQHSVEV*ILFVTGVHEEATEEDIHD

Parental  KFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP-KGKRR
          K..EYG.I.NIHLNLDR.TG.LK.YTL.EYETYKE.QAA.EGLNGQDLMGQPIS..WCFV.G.P.KG.RR
Retrocopy KLSEYG*IINIHLNLDRHTGCLKEYTLAEYETYKEDQAAIEGLNGQDLMGQPISIHWCFVCGSP<KGRRR

Parental  GGRR
          ..RR
Retrocopy RSRR

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	18.12 RPM
SRP017611_kidney	0.00 RPM	22.33 RPM
SRP017611_liver	0.00 RPM	12.91 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1828 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1828 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016021	1 retrocopy	retro_dnov_47,
Echinops telfairi	ENSETEG00000008411	1 retrocopy	retro_etel_1200,
Felis catus	ENSFCAG00000026379	1 retrocopy	retro_fcat_955,
Homo sapiens	ENSG00000131795	1 retrocopy	retro_hsap_1349,
Macropus eugenii	ENSMEUG00000016058	2 retrocopies	retro_meug_873, retro_meug_952,
Myotis lucifugus	ENSMLUG00000017436	2 retrocopies	retro_mluc_179, retro_mluc_1932,
Mus musculus	ENSMUSG00000038374	2 retrocopies	retro_mmus_137, retro_mmus_776,
Otolemur garnettii	ENSOGAG00000000202	2 retrocopies	retro_ogar_2694, retro_ogar_771,
Ochotona princeps	ENSOPRG00000013316	2 retrocopies	retro_opri_1146, retro_opri_659,
Rattus norvegicus	ENSRNOG00000021215	2 retrocopies	retro_rnor_1434, retro_rnor_1828 ,
Sorex araneus	ENSSARG00000013289	2 retrocopies	retro_sara_116, retro_sara_217,
Tupaia belangeri	ENSTBEG00000014947	2 retrocopies	retro_tbel_3548, retro_tbel_804,