RetrogeneDB ID: retro_rnor_1276

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:62228543..62229700(+)
• Located in intron of: ENSRNOG00000018905

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000013691
• Aliases: None
• Description: None

Sequence

>retro_rnor_1276
TTTGGAGGGAGTAGAACAGGACTCCTCTCTGGAAAGAAGTTTGGAATTCCTGGGGGAGAAACAAGTTAAAAAGAAGTGGA
ATCTTGATGAGCTGCCCAAATTTGAGAAGAATTTTTATCAGGAATACCCTGATTTGGCAAGGCACACCACACAAGAGGTA
GATACATACAGGGGAAGCAAGGAAATTACAGTTATTGGTCACAACTGTCGAAAACCTGTTTGAATTTTTATGAAGCAAAC
TTTCCCGAGAATGCCATGGATGTGATTGCAAGGCCATCACAAGAACTTCACTGAACCCACTGCTATTCCAGCTCAGGGCT
GGGCATTGCTCTCAGTGTGGATATGGTTGGAGTAGCTCTGACTGGATCTGGGAAAACATTATCTTATTTGCTGCCTATCA
TTGTACACAAGAACCACCAGCCATTCCTAGAGAGAGGTGATGGGCACATTTGTTTGGAGCTGGCACCAACTCGAGAACTG
GCACAGCAGGTGCAGGAAGTCGTGGCTGAATATCGTAGAGCTCATCATTTGAAGTCTATTTGCATCTATGCTGGTGCTCC
CGAAGGACCACAGATTCATAATTTGGAAAGAGGTGTGGAACTCTGTATCGCAACACCTGGAACATTGATCGACTTTTTAG
GGTGTGGGGAAACAAATTTGAGAAGAACAACTTACCTTGTCCTTGGTGAAGCTGATAGGATGCCCGATATGGGATTTGAA
CCCTAAATAAGGAAAATGGTGGATCCAATAAGACCTGATAGGCAAACACTAATGTGGAGTACAACTTGGCCAAAAGAAGT
AAGACAACTTGCTAAAGATTTCCTGAAAGACCACGTTCGTATCAATAGTGATGCACTGGGACTGAGTGCAAACCGTAACA
TTCTTCAGATTGTCGATGTGTCATGACGTCAAAAAGGATGGAAAAACGTTTTCGTCTGATGGAAGAGACCATGAGTCACA
AGGAGAATAAAAACATTGTTTTTGTTAAAATCAAAAGAAGATGTGATGAACTTAACAGAAAAATGAGGGGAGATGGGTGG
GCTGCCAAGGGCACCCATGGTGACAAGAGTCAGCAGGAACATGACTGGGTTCTAAATAAATTCAAACACGGAAAAGCTCC
TATTCTGGTTGCTACCGATGTGGCCTCCAGAGGGCTA

Alignment

ORF - retro_rnor_1276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.5 %
• Parental protein coverage: 92.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FGARGGSGLPPKKFGNPG-ERLRKKKWDLSELPKFEKNFYVEHPEVARLTPYEVDELRRKKEITVRGGDV
          FG......L..KKFG.PG.E...KKKW.L.ELPKFEKNFY.E.P..AR.T..EVD..R..KEITV.G...
Retrocopy FGGSRTGLLSGKKFGIPG>EKQVKKKWNLDELPKFEKNFYQEYPDLARHTTQEVDTYRGSKEITVIGHN-

Parental  CPKPVFAFHHANFPQYVMDVLMDQH--FTEPTPIQCQGFPL-ALSGRDMVGIAQTGSGKTLAYLLPAIVH
          C.KPV..F....FP......L...H..FTEPT.I..QG..L.ALS..DMVG.A.TGSGKTL.YLLP.IVH
Retrocopy CRKPV*IFMKQTFPRMPWM*LQGHHKNFTEPTAIPAQGWAL<ALSV-DMVGVALTGSGKTLSYLLPIIVH

Parental  INHQPYLERGDGPICLVLAPTRELAQQVQQVADDYGKCSRLKSTCIYGGAPKGPQIRDLERGVEICIATP
          .NHQP.LERGDG.ICL.LAPTRELAQQVQ.V...Y.....LKS.CIY.GAP.GPQI..LERGVE.CIATP
Retrocopy KNHQPFLERGDGHICLELAPTRELAQQVQEVVAEYRRAHHLKSICIYAGAPEGPQIHNLERGVELCIATP

Parental  GRLIDFLESGKTNLRRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLR
          G.LIDFL..G.TNLRR.TYLVL.EADRM.DMGFEP.IRK.VD.IRPDRQTLMWS.TWPKEVRQLA.DFL.
Retrocopy GTLIDFLGCGETNLRRTTYLVLGEADRMPDMGFEP*IRKMVDPIRPDRQTLMWSTTWPKEVRQLAKDFLK

Parental  DYTQINVGNLELSANHNILQIVDV-CMESEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLTRRMRRD
          D...IN...L.LSAN.NILQIVDV..M.S....K...LMEE.M..KENK.I.FV..KRRCD.L.R.MR.D
Retrocopy DHVRINSDALGLSANRNILQIVDV<VMTSKRMEKRFRLMEETMSHKENKNIVFVKIKRRCDELNRKMRGD

Parental  GWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGL
          GW.A...HGDKSQ.E.DWVLN.F..GKAPIL.ATDVASRGL
Retrocopy GWAAKGTHGDKSQQEHDWVLNKFKHGKAPILVATDVASRGL

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	118.27 RPM
SRP017611_kidney	0.00 RPM	119.61 RPM
SRP017611_liver	0.00 RPM	84.05 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1276 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1276 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006499	1 retrocopy	retro_dnov_1903,
Otolemur garnettii	ENSOGAG00000001539	1 retrocopy	retro_ogar_3395,
Rattus norvegicus	ENSRNOG00000013691	1 retrocopy	retro_rnor_1276 ,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,