RetrogeneDB ID: retro_rnor_20

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:29913532..29914930(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000025637
• Aliases: LOC317471, Fam154a
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Fam154a
• Ensembl ID: ENSRNOG00000048197
• Aliases: None
• Description: None

Sequence

>retro_rnor_20
ATGGCTCTCATGAATAGGAAGTGCATTTGTGACCTTTGCTCTTGTGGCAAGCATCACTGCCCACATCTCCCTACCAAGAT
TTATGAGAAGACAGAGAAACCATGTTTCTTCTCCGAATACACCGAGAAGTATCCTACCTATCTTTCTTATGTGCCCCGAG
AGTCCTTCAAACCCAAGTTGGAGTACCAGAAAGTAAATATACCAATGGAAGGCCTGTCCACAACGAAGAGAGACTTTGGA
ACCTTCAACATAGTACCAGTGAAACACCATCTTCCTGAGAAGGCCACTCCAATCCAAGACGAAATGGATTTCCTCACAAC
GTATAATCAACACTACAACTACTGCCCTGCCAATCGAGTGAACCCCATCAAACCTCGAGACAACAAACATCAATGTAATG
ACAAAATGGAGTGTGTGCCTACGTACAAAGCTGATTATTTGCCCTGGAACCAACAAAAGAGATCTTCGATTCGTCCACCA
CAATCATACCGTCCTGCGTCCTGTAGGTTTGATCATAGAACCACACACCAGGACGATTATCCCATAAAAAATCCTGTGGA
TACTGTGAGTTACAAACCTCCACATGGGCCCAAGCTGTGCAACATCCCCTTGGAGAGTATGACAAGTTACAAATCGAGCT
ATGTGGCCCATCCCATGGAGAAGCGGTGTGTGTATGAGGGAGAGAAGTATAAACCAAGTGAAGTCCCTTTTGATAGCCTT
ACCACCCACAAAGATTCCTACAGGGGTTTGATCGGGGAGCCTGCCAAGACCTGGAAACCTGCCCCAAATCACCCTGGGCT
GGATATACCTTTTCCATCCAACACTGAATTCCGAGAAAAATTCCAACCTTGGCCAACACCCAAGATTGTCCCCAAAGAGT
CCATTGCCTACATCCCTCCTGAAGGGAAGATGGATCTTCTAACAACTGTGCAAGCAGACTACAAGTGCCCCAATGGTGTT
CCTGCTCAGTCCTGCCGGCCAGTCATCCATTTGAAGAAGAGTGACCGATTTGAAAGCTCTACGACCAACAGAGAGGATTT
TAAACACTGGGCCAACATCCGAAGAGAGCCAGTCAAACCTAATCACCAGCTGAAATTCTCTGATGAACCTATGGAATACA
TGACCACCAATCGTGCCCACTATGTGCCTCATGCACCAGCCAATACCAAAAGCTGCAAGCCAACCTGGTCTGGCCCTCGT
GTAAACATCCCTTTAGAAGGCCAGACCACCTACTCTACCAGTTTTACTCCTAAGGAAATTCAAAGGTGCCCAGCTTCATA
CCCTGAACCCCCTGGCTACATCTTTGATGAGGTGGATGCTGTAGGGCACAGGCTGTACAGGCCGGCTTCCGGAGCAACTT
CTCAAGAGAGCAACCATCTTGGCTTTGGTGATGCATAA

Alignment

ORF - retro_rnor_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.32 %
• Parental protein coverage: 97.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CRRHRCPHLPTKIYDKTEKPSLLSEYTENYPIYESYLPRNSFKPECAYQKASIPMEGLTTSRRDFGLHKM
          C..H.CPHLPTKIY.KTEKP...SEYTE.YP.Y.SY.PR.SFKP...YQK..IPMEGL.T..RDFG....
Retrocopy CGKHHCPHLPTKIYEKTEKPCFFSEYTEKYPTYLSYVPRESFKPKLEYQKVNIPMEGLSTTKRDFGTFNI

Parental  LPVKFYQPAAYVPSQESMNLLTSYKHDFNYIPTCPVGLIKPRDSKFPNGDKTVQYLPTYKVDYVPWNQPR
          .PVK...P....P.Q..M..LT.Y....NY.P...V..IKPRD.K....DK.....PTYK.DY.PWNQ..
Retrocopy VPVKHHLPEKATPIQDEMDFLTTYNQHYNYCPANRVNPIKPRDNKHQCNDK-MECVPTYKADYLPWNQQK

Parental  RELLRPPHKYRPESAKFENRTTHQDDYTMKCLVTTESCKPSVKAKICNIPLEDLTNYKMSYVPHPVEKRF
          R...RPP..YRP.S..F..RTTHQDDY..K..V.T.S.KP....K.CNIPLE..T.YK.SYV.HP.EKR.
Retrocopy RSSIRPPQSYRPASCRFDHRTTHQDDYPIKNPVDTVSYKPPHGPKLCNIPLESMTSYKSSYVAHPMEKRC

Parental  VKEAEKYIPCDIPFENLTTHKESYRGLLGEPAKSSKPPGKIPVHDVPFSDITEIQEKYQAWPTPQIVPKA
          V.E.EKY.P...PF..LTTHK.SYRGL.GEPAK..KP....P..D.PF...TE..EK.Q.WPTP.IVPK.
Retrocopy VYEGEKYKPSEVPFDSLTTHKDSYRGLIGEPAKTWKPAPNHPGLDIPFPSNTEFREKFQPWPTPKIVPKE

Parental  PVVYVPPEEKMDLLTTVQTHYKHRKGSPAITCRPVPSIKKSGRFQSSTTSKDDFKQWAAVNTKPIRPVPH
          ...Y.PPE.KMDLLTTVQ..YK...G.PA..CRPV...KKS.RF.SSTT...DFK.WA.....P..P...
Retrocopy SIAYIPPEGKMDLLTTVQADYKCPNGVPAQSCRPVIHLKKSDRFESSTTNREDFKHWANIRREPVKPNHQ

Parental  LNLPVEPLDCQTTTKICYVPHPPTITENYKPAWVGPRRNIPVEGQTTYSISFTPKDLGRCPASYINPPGY
          L....EP....TT....YVPH.P..T...KP.W.GPR.NIP.EGQTTYS.SFTPK...RCPASY..PPGY
Retrocopy LKFSDEPMEYMTTNRAHYVPHAPANTKSCKPTWSGPRVNIPLEGQTTYSTSFTPKEIQRCPASYPEPPGY

Parental  IFEEVDSTGHKIYRSISQTASRQNSSLSIHD
          IF.EVD..GH..YR..S...S.....L...D
Retrocopy IFDEVDAVGHRLYRPASGATSQESNHLGFGD

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	0.00 RPM
SRP017611_kidney	0.07 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_20 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_20 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_20 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3727

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028492	1 retrocopy	retro_mmus_3727,
Rattus norvegicus	ENSRNOG00000048197	1 retrocopy	retro_rnor_20 ,