RetrogeneDB ID: retro_rnor_1373

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:84766154..84767349(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpa1
• Ensembl ID: ENSRNOG00000003123
• Aliases: Rpa1, Cb1-727
• Description: replication protein A 70 kDa DNA-binding subunit [Source:RefSeq peptide;Acc:NP_001041308]

Sequence

>retro_rnor_1373
ATGCAGCAGGAAGATACATCCATAAAACCCATCCTTCAAGTCATTAACATCTGTCCCATTACTACCAGGGAATAGTCCAC
CCTGGTAATGACTGCTTATGAGTGATGCATTGAACATGCTTTCCTCTTTCATGTTGGCCATGCCACTGAATGCCCTGGTC
ATGGGGGGACAGCTGGCCAGCAGCTGTGTCTGTCAGGTCAACTGGTACATCGTCAACACCCTAAAGATGGAGGGAGTCGT
TATTTTGATGGACTCGGAGGTTGTGGAATCTGCCGATGAAGTTGAATTAAAGATTGGGAATCCAGTGCCCTATATTGAAG
AACATGGGCAGCAGCAAGTAGTCTCTTTCCCAGCCTCTGCAGCAACTCCACCAGCCAGCAAGCCCCAGTCGCAGAATGGG
AGCTTGGGAATGGGTTCCACTGAGGCTTAACGTGCCTCAAAGCCATTTGGAAAACCTGCTGGAACTGGCCTGCTGTAGCC
TTCAGGTGGGACCCCATTCAAAGCGGTGACCATCGACAGCCTCAGCCCTTACCAATTCAAGTGGACTATTTATGCCCATG
TCACTAACAAAAGTCAGATCTGTACCTGGAGCAATTCCCACGTGGAAGGAAAGCTTTTCTCTATAGAACTTGTAAATTTA
AGTGGTGAAATCAGAGCTACTGCTTTCAATGAGCAGGTGAACAAGTTCTTTCCCCTTGTTGAAGTGAACAAAGTATATTA
CTTCTCAAAGGGCACTCTGAAGATTGCTAATAAACAATTCTCAGTGGTTAAAAATGACTATGAGATGACCTTCAATAACG
AGACTTCTGTCCTTCCGTGTGAAGGTGGTCATCACTTATCCACAGTTCAGTTTGATTTCACAGGGATCGGTGACCTAGAG
AGCAAGTCTAAAGACTCATTTGTAGACATAATTGGAATCTGCAAGAGCTATGAAGATTGAACTAAAATCACAGTGAAGTC
TAACAACACAGAAATTGCTAAGAGAAATATCTATTTGATGAACATGTCAGGGAAAATGGTGACTATGATTCTGTAAGGAG
AAGACGCTGACAAATTTGATGGTTTTAGGCAGCCTGTGATGGCTATCAAAGAAGCCTGAGTTTCTGACTTTGGTGGACAG
AGCCTCTTGGTCCTATCATCTAGCCCTGTCATTTTGAATCCTGACATCCTAGAGGCACATAAGCTCTATGGATGG

Alignment

ORF - retro_rnor_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.1 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQQGDTSIKPVLQVINIRPITT-GNSPPRYRLLMSDGLNTLSSFMLATQLNALVEGGQLASNCVCQVHRF
          MQQ.DTSIKP.LQVINI.PITT.GNSPP...LLMSD.LN.LSSFMLA..LNALV.GGQLAS.CVCQV...
Retrocopy MQQEDTSIKPILQVINICPITT>GNSPPW**LLMSDALNMLSSFMLAMPLNALVMGGQLASSCVCQVNWY

Parental  IVNTLKDGRRVVILMDLEVVKSAGEVGVKIGNPVPYNEGHAQQQAVSAPASAATPPASKPQPQNGSLGVG
          IVNTLK....VVILMD.EVV.SA.EV..KIGNPVPY.E.H.QQQ.VS.PASAATPPASKPQ.QNGSLG.G
Retrocopy IVNTLKM-EGVVILMDSEVVESADEVELKIGNPVPYIEEHGQQQVVSFPASAATPPASKPQSQNGSLGMG

Parental  STVAKAYGASKPFGKPAGTGLLQPTSGTQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLF
          ST...A..ASKPFGKPAGTGLL.P..GT..K.V.I.SL.PYQ.KWTI.A.VTNKSQI.TWSNS..EGKLF
Retrocopy ST--EA*RASKPFGKPAGTGLL*PSGGTPFKAVTIDSLSPYQFKWTIYAHVTNKSQICTWSNSHVEGKLF

Parental  SIELVDESGEIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFSAVKNDYEMTFNNETSVLPCEDG
          SIELV..SGEIRATAFNEQV.KFFPL.EVNKVYYFSKGTLKIANKQFS.VKNDYEMTFNNETSVLPCE.G
Retrocopy SIELVNLSGEIRATAFNEQVNKFFPLVEVNKVYYFSKGTLKIANKQFSVVKNDYEMTFNNETSVLPCEGG

Parental  HHLPTVQFDFTGIGDLESKSKDSLVDIIGICKSYEDATKITVKSNNREVAKRNICLMDMSGKVVTATLWG
          HHL.TVQFDFTGIGDLESKSKDS.VDIIGICKSYED.TKITVKSNN.E.AKRNI.LM.MSGK.VT..L.G
Retrocopy HHLSTVQFDFTGIGDLESKSKDSFVDIIGICKSYED*TKITVKSNNTEIAKRNIYLMNMSGKMVTMIL*G

Parental  EDADKFDGSRQPVMAIKGARVSDFGGRSLSVLSSSTVLVNPDIPEAYKLRGW
          EDADKFDG.RQPVMAIK.A.VSDFGG.SL.VLSSS.V..NPDI.EA.KL.GW
Retrocopy EDADKFDGFRQPVMAIKEA*VSDFGGQSLLVLSSSPVILNPDILEAHKLYGW

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	26.60 RPM
SRP017611_kidney	0.00 RPM	41.59 RPM
SRP017611_liver	0.00 RPM	21.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1373 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013540	2 retrocopies	retro_chof_167, retro_chof_2578,
Rattus norvegicus	ENSRNOG00000003123	1 retrocopy	retro_rnor_1373 ,
Ictidomys tridecemlineatus	ENSSTOG00000022475	1 retrocopy	retro_itri_677,