RetrogeneDB ID: retro_rnor_686

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:45717396..45718129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sbds
• Ensembl ID: ENSRNOG00000000888
• Aliases: None
• Description: Ribosome maturation protein SBDS [Source:UniProtKB/Swiss-Prot;Acc:Q5RK30]

Sequence

>retro_rnor_686
TCGATCTTCACCCCCACCAACCAGATCTGATTGACCAGTGTGGCCATGGTGTGGGTGAAGCGGGGAGGGAAGCGCTTCGA
AGTTGCCTGCTATAAAAACAAGGTCTTCAGCTGGCGGGAGTGGCATGGAAAAAGGCCTTGATGAAGTTCTGCAGACCCAT
TCAGTGTTTGTCAATGTTTCCAAAGGTCAGATTGTCAAGAAGGAAGACTTCATCAGTGGGACAGACGACCAGACTGAAAT
CTGCAAACAGATTTTGACTAAAGGAGAAGTTCAAGTGTCAGATAAAGAACGGCACACACAGCTGGAGCAGATGTTTAGGG
ATATTGCCACCATTGTGGCACACAAGTATGTGTGAACCCAGAAACAAAGAGACCCTACCTACACCGTTATCCTCATCGAG
AGAGCCATGGAGGACATCCACTACTCTGTCAAACTCAACAAGAGCACCAAGCAGCGGGCTTTGGAGGAGATAAAGCAGCT
GAAAGAGAAGATGAAGACAGAGCGGGCCCACATGCGCATGCGCTTTATCCTGCGGGTGAACGAAGGGAAGAAACTGAAGG
AAAAGCTGAAGCCACTGATGAAGGTCGTGGAGAGTGAGGACTAAAGCCAGCGGCTGGAGATCGTATGCCTCATCGACCCA
GGCTGCTTCAGAGAAACTGATGAGCTGATAAAAAAGGAAACCAAAGGCAAGGGTTCTGTGGAAGTGCTCTGTCTGAAAGA
CGTGGAGGAAGGA

Alignment

ORF - retro_rnor_686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 97.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIFTPTNQIRLTNVAVVRMKRGGKRFEIACYKNKVVGWR-SGVEKDLDEVLQTHSVFVNVSKGQVAKKED
          SIFTPTNQI.LT.VA.V..KRGGKRFE.ACYKNKV..WR.SG.EK.LDEVLQTHSVFVNVSKGQ..KKED
Retrocopy SIFTPTNQI*LTSVAMVWVKRGGKRFEVACYKNKVFSWR>SGMEKGLDEVLQTHSVFVNVSKGQIVKKED

Parental  LISAFGTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRP--YTVILIERAMK
          .IS..GTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVA.K.V.....R...YTVILIERAM.
Retrocopy FIS--GTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVAHKYV*TQKQRDPTYTVILIERAME

Parental  DIHYSVKPNKSTKQQALEVIKQLKEKMKIERAHMRLRFLLPVNEGKKLKEKLKPLMKVVESEDYSQQLEI
          DIHYSVK.NKSTKQ.ALE.IKQLKEKMK.ERAHMR.RF.L.VNEGKKLKEKLKPLMKVVESED.SQ.LEI
Retrocopy DIHYSVKLNKSTKQRALEEIKQLKEKMKTERAHMRMRFILRVNEGKKLKEKLKPLMKVVESED*SQRLEI

Parental  VCLIDPGCFREIDELIKKETKGKGSLEVLSLKDVEEG
          VCLIDPGCFRE.DELIKKETKGKGS.EVL.LKDVEEG
Retrocopy VCLIDPGCFRETDELIKKETKGKGSVEVLCLKDVEEG

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	50.11 RPM
SRP017611_kidney	0.00 RPM	74.04 RPM
SRP017611_liver	0.00 RPM	20.51 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_686 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_686 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_686 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
Choloepus hoffmanni	ENSCHOG00000003795	2 retrocopies	retro_chof_1999, retro_chof_623,
Callithrix jacchus	ENSCJAG00000004283	1 retrocopy	retro_cjac_3984,
Dasypus novemcinctus	ENSDNOG00000016904	1 retrocopy	retro_dnov_748,
Loxodonta africana	ENSLAFG00000008763	1 retrocopy	retro_lafr_920,
Monodelphis domestica	ENSMODG00000006644	1 retrocopy	retro_mdom_2004,
Mus musculus	ENSMUSG00000025337	1 retrocopy	retro_mmus_950,
Otolemur garnettii	ENSOGAG00000009011	1 retrocopy	retro_ogar_3368,
Ochotona princeps	ENSOPRG00000008721	6 retrocopies	retro_opri_1179, retro_opri_154, retro_opri_363, retro_opri_484, retro_opri_698, retro_opri_957,
Rattus norvegicus	ENSRNOG00000000888	1 retrocopy	retro_rnor_686 ,
Ictidomys tridecemlineatus	ENSSTOG00000022203	1 retrocopy	retro_itri_1763,