RetrogeneDB ID: retro_rnor_1182

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:19667414..19668438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rbbp7
• Ensembl ID: ENSRNOG00000005157
• Aliases: None
• Description: Histone-binding protein RBBP7 [Source:UniProtKB/Swiss-Prot;Acc:Q71UF4]

Sequence

>retro_rnor_1182
CAAGTTCATATTCCCAATGATGATGCGCAGTTTGATGCTTCCCATTGTGACAGTGACAAGGGAGAATTTGGTGGCTTTGG
TTCTGTAACAGGAAAAATTGAATGTGAAATTAAAATTAATCACAAAGGAGAAGTAAATTGAGCTCGTTATATGCCACAGA
ATCCTCACATCATTGCCACAAAAACTCCATCTTCTGACGCTTTTGGTTTTTGACTATACAAAACACCCTGCAAAACCAGA
TCCAAGTGGAGAAGGTAATCCTGATGTTAGATTGGTGGGTCACCAAAAGGAAGGCTATGGTCTTTCCTGGAATTCTATTT
TGAGTGGACATCTCCTGAGTGCATCTGATGACCATACTGTCTGCCCCTGGGATATAAATGCAGGATCAAAGGAAGGCCAG
ATTGTGGATGCTGAAGCAATCTTTGCTGGCCGATCAGCTGTTGTAGAGGATGTGGCCTGGCATCTGCTGCATGAGTCCTC
GTCTGGATCTGTTGCTGATGATCAGAAACTTATGACACGGGACACCAGATCCAATACTACTTCTAAGTGGAGCCATTTGG
TGAACGAGCACACTGCAGAGGTCAACTGCCTCTCATCCAAGCCCGATAGGGAGTGCATTCTAGCAAATGGCTCTGCAGAG
AAGACTGTAGCTTCATGGGACCTGCGCGATCTGAAACTAAAGCTCCATACCTTGGAATCCCACAAGGATGAGACTTTTCA
GGTCCATTGGTCTCCACATAATCAAACTATTCTGGCTTCAAGTGGTGCTGATCGCCGCCTGGATGTGTGGAATTTAAGTA
AAATTGGAGAAGAACAATCAGCAAAAGATGGGTCTCCAGAGCTCCTGTCTATTCACGGAGGACACACTGCCGAGATTTCT
GACTTCAGTTGGAACCCCAGTGAACCTTGGGTCATTTTCCCTGTGTCTGAAGATAACACCGTGCAGACATGGCGAATGGC
TGAAAATATTTACAATGATGAAGAGTCAGATGTCATGACAGCGGAACTGGAGGGGCAAGGATCT

Alignment

ORF - retro_rnor_1182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.64 %
• Parental protein coverage: 80.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHIIATKTPSSD-VLV
          .VHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINH.GEVN.ARYMPQNPHIIATKTPSSD..LV
Retrocopy QVHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHKGEVN*ARYMPQNPHIIATKTPSSD>LLV

Parental  FDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKIVDAKA
          FDYTKHPAKPDPSGE.NPD.RL.GHQKEGYGLSWNS.LSGHLLSASDDHTVC.WDINAG.KEG.IVDA.A
Retrocopy FDYTKHPAKPDPSGEGNPDVRLVGHQKEGYGLSWNSILSGHLLSASDDHTVCPWDINAGSKEGQIVDAEA

Parental  IFTGHSAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPYSEFILAT
          IF.G.SAVVEDVAWHLLHES..GSVADDQKLM..DTRSNTTSK.SHLV..HTAEVNCLS..P..E.ILA.
Retrocopy IFAGRSAVVEDVAWHLLHESSSGSVADDQKLMTRDTRSNTTSKWSHLVNEHTAEVNCLSSKPDRECILAN

Parental  GSADKTVALWDLRNLKLKLHTFESHKDEIFQVHWSPHNETILASSGTDRRLNVWDLSKIGEEQSAEDAED
          GSA.KTVA.WDLR.LKLKLHT.ESHKDE.FQVHWSPHN.TILASSG.DRRL.VW.LSKIGEEQSA.D...
Retrocopy GSAEKTVASWDLRDLKLKLHTLESHKDETFQVHWSPHNQTILASSGADRRLDVWNLSKIGEEQSAKD---

Parental  GPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQIWQMAENIYNDEESDVTTSELEGQGS
          G.PELL.IHGGHTA.ISDFSWNP.EPWVI..VSEDN..Q.W.MAENIYNDEESDV.T.ELEGQGS
Retrocopy GSPELLSIHGGHTAEISDFSWNPSEPWVIFPVSEDNTVQTWRMAENIYNDEESDVMTAELEGQGS

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	0.29 RPM	94.33 RPM
SRP017611_kidney	0.07 RPM	96.44 RPM
SRP017611_liver	0.00 RPM	41.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1182 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1182 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002820	1 retrocopy	retro_btau_1579,
Mus musculus	ENSMUSG00000031353	1 retrocopy	retro_mmus_3529,
Oryctolagus cuniculus	ENSOCUG00000000683	1 retrocopy	retro_ocun_1939,
Otolemur garnettii	ENSOGAG00000014995	1 retrocopy	retro_ogar_2220,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pan troglodytes	ENSPTRG00000021702	5 retrocopies	retro_ptro_1802, retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,
Rattus norvegicus	ENSRNOG00000005157	1 retrocopy	retro_rnor_1182 ,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sorex araneus	ENSSARG00000008079	3 retrocopies	retro_sara_308, retro_sara_571, retro_sara_602,
Tupaia belangeri	ENSTBEG00000010151	2 retrocopies	retro_tbel_3031, retro_tbel_4341,
Tarsius syrichta	ENSTSYG00000002385	4 retrocopies	retro_tsyr_1608, retro_tsyr_1838, retro_tsyr_1957, retro_tsyr_427,