RetrogeneDB ID: retro_rnor_2805

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:63111925..63113047(+)
• Located in intron of: ENSRNOG00000013322

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slc30a9
• Ensembl ID: ENSRNOG00000002246
• Aliases: None
• Description: zinc transporter 9 [Source:RefSeq peptide;Acc:NP_001102558]

Sequence

>retro_rnor_2805
GCAGTGGCCCACGGCTGCAGCCAGGGATGGGAGAATTTACTGACATTTGAAAGCTTTACATACATGATTCCCAAAATTCG
CTCACATATATCTATTCTAAATCAAGTCCAAGTTGTACTCTACAAATGTCCAGAAAGTAGGGCAGAACTCACAAACTCCA
AGAGCTGATAAAGTCCCATCACTTATGCAAACAGCAGAAAACATAGGCACAGAACGCAAAGCTCCACTTAAGGAAGATCC
TCTCCAAATAAGAGTCAAAGCAGTCCTTAAGGAAAAGGAGTACAGATAAAAATACACTAAGAATAATTTCATCACTGGAC
TAAGAGCAATAAGTGAGTTCTGACTTCAGTTCAGTGATTTAGAACAACTTGGAAAACTCAGGCAACAAAGCCCCCATGAT
GACACTGAGTCCTTCACTGTGTTCTTGCGGTCAGATGTGAAAGCAAAAGCTCTGGGCGTTTGGGGAAGCCTTGAAGCTCT
TGGCAGAGAGAAAAAATGCGTAAAGAAACAGAAATAGAATACACAGAGTGGCTGTTTAGAAAGCAAAGAATACTAAGAGA
ATATGGTGATTTCTTGGAAATAAAAAGCCACACTTCAGAACGGTCTCAGTGTTCCTTAAGGGAGCAGGGTGGTGGTTGCT
ATTTCCATTAATGGCTTAAACAGCTTCTTTAAATTTCTTGCCTGGATTTGTACGGCTTCAGCAATGTGTTCTCAGAAGCT
ATACCCTCATTATCTGATACTTATACCGTGCGTTTGCTAGCACTGAGCATCAGCAAGTCTGTTCAAACACTAGATCCTTC
TTACCAGGACGGCTTTTCAAATATGTGCTATGTTTCTTCATTGATTAATGGTGTTGGTATTTTCATGATGGGCACAGGAC
TCTGCTGGTATCACGGAATCATGGGATTGCTTCATCCTCAACCAATATAATCCTTTCTATGGGCATATTGTATTTTATCA
GGATCTTTGGTGTCTGAAGGAACAATAACTCTTGTTGCCACAACTGAACTTCATAGGAGCACACAGGTCAAGGGAATATC
ATTTTATAAGTATGTTATGGAGAGCCATGATCTGAGAACAAATGTTATTCTATTGGAGGACACTGCAGCTGTCTTAGGAC
TG

Alignment

ORF - retro_rnor_2805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.61 %
• Parental protein coverage: 66.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AVARGRSQGWKNLMTFESFTSMIPSIHPQISVLNQV-KLYSTNVQKGGQGSQTPRTDKAPPLTQAAENIG
          AVA.G.SQGW.NL.TFESFT.MIP.I...IS.LNQV.KLYSTNVQK.GQ.SQTPR.DK.P.L.Q.AENIG
Retrocopy AVAHGCSQGWENLLTFESFTYMIPKIRSHISILNQV>KLYSTNVQKVGQNSQTPRADKVPSLMQTAENIG

Parental  AELKAPLKQDPLQVRVKAVLKKREYGSKYTKNNFITGVRAINEFCLKSSDLEQLRKIRRRSPHDDTESFT
          .E.KAPLK.DPLQ.RVKAVLK..EY..KYTKNNFITG.RAI.EF.L..SDLEQL.K.R..SPHDDTESFT
Retrocopy TERKAPLKEDPLQIRVKAVLKEKEYR*KYTKNNFITGLRAISEF*LQFSDLEQLGKLRQQSPHDDTESFT

Parental  VFLRSDVEAKALEVWGSLEALAREK-KLRKEAEIEYRERLFRNQRILREYGD-FLGNTKPRSRAISVFLK
          VFLRSDV.AKAL.VWGSLEAL.REK.K.RKE.EIEY.E.LFR.QRILREYGD.FLGN.KP..R..SVFLK
Retrocopy VFLRSDVKAKALGVWGSLEALGREK<KMRKETEIEYTEWLFRKQRILREYGD<FLGNKKPHFRTVSVFLK

Parental  GPG-KVVMVAICINGLNCFFKFLAWIYTGSA-SMFSEAIHSLSDTCNQGLLALGISKSVQTPDPSHPYGF
          G.G..VV...I..NGLN.FFKFLAWI.T.SA...FSEAI.SLSDT....LLAL.ISKSVQT.DPS...GF
Retrocopy GAG<VVVAISI--NGLNSFFKFLAWICTASA<NVFSEAIPSLSDTYTVRLLALSISKSVQTLDPSYQDGF

Parental  SNMRYISSLISGVGIFMMGAGLSWYHGIMGLLHPQPMESLLWAYCILAGSLVSEGATLLVAINELRRSAQ
          SNM.Y.SSLI.GVGIFMMG.GL.WYHGIMGLLHPQP..S.LWAYCIL.GSLVSEG...LVA..EL.RS.Q
Retrocopy SNMCYVSSLINGVGIFMMGTGLCWYHGIMGLLHPQPI*SFLWAYCILSGSLVSEGTITLVATTELHRSTQ

Parental  ANGTSFYKYVMESRDPSTNVILLEDTAAVLGV
          ..G.SFYKYVMES.D..TNVILLEDTAAVLG.
Retrocopy VKGISFYKYVMESHDLRTNVILLEDTAAVLGL

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	153.00 RPM
SRP017611_kidney	0.00 RPM	86.39 RPM
SRP017611_liver	0.00 RPM	33.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2805 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2805 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019226	1 retrocopy	retro_cjac_408,
Cavia porcellus	ENSCPOG00000000374	1 retrocopy	retro_cpor_805,
Otolemur garnettii	ENSOGAG00000000501	1 retrocopy	retro_ogar_3376,
Rattus norvegicus	ENSRNOG00000002246	1 retrocopy	retro_rnor_2805 ,
Sus scrofa	ENSSSCG00000008801	1 retrocopy	retro_sscr_326,
Ictidomys tridecemlineatus	ENSSTOG00000024271	1 retrocopy	retro_itri_658,