RetrogeneDB ID: retro_rnor_396

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:99094554..99096000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000024884
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RGD1561226
• Ensembl ID: ENSRNOG00000048835
• Aliases: None
• Description: None

Sequence

>retro_rnor_396
ATGAGTGTTCAGACCCCACCCACACTCCAGGAGCTGACAGTGCATAGTCTGCTGAGAAATGAGGCCATGGCCATGTCCTA
TCTTGGGGAGCTCCCTGCTGTGCTCTTCCCAAAAGTGTTCAAGGAGGCATTTGCTAGAAGACACAACAATCTAGTGAAGG
AAATGGTGGCAGTTTTACCTTTCCCCTGTCTCCCAGTGGGGGCACTCATGGAGATACCCAACCTGAAAACCTATCAGGCT
TTGCTAGATGGAATAGACATGGGACTGAAAGAAGAGTTTCACCACAGGGAGAAAAATCTTAAGATCTTGGACCTGAGAAA
TGTGCACCATGCCTTCTGGAATATATGTGCTGGTGAAGGGAAGAGTAGCTGTTCATCAGAGACACTGGACAAGAAGCAAG
TAGTGAAGGTCTTTCCCAGATATGTACTGAGACAGCGTCTGAGGGTCATAGTTGACCTGTGCCTCAAACTAAGCCTCAAT
GAAGCACAAGCATACTTCTTGAGTTGGGTCCAGCAAAGGAAGAGCTCCCTTTATTTCTGCTATATAAAAATGACAATCTG
GTCTCTCCCATTCCAAGATATCAAAGGGATCTTGAATGTTTTTGACACAGAGCACATTACAGAATTAGAACTGCATACCA
AGTGGACTCTGTTACAGCTGGGATATTTTGCTCACTACTTTGGACAGATGAGAAATCTTCGCAAACTTATCCTGGCACCC
CTCCATATGAGAACCTTCTCTACTGTCGAAAGAACAATGGTCAGAGAAACCAGGAGTGTCAACAATTTTATTTCTCAGTT
CTCTCAATTCAACTGTCTGCAGCATCTCTTCATAAGTCAAGTTCATTTCCTCAGAGTCCAGATGAATCAGATTTTAGGGT
GCCTGATGACGCGCTTGGAGACCCTCTCTGTCACTAATTACGTAACTTCACAGGGAAACTTGAATTCCTTCGCCTGCTGT
CAGAGCCTCTTTCAGTTAAAACATCTGGATCTGAGAGAAACAGTTTTGTATTCACTGGATCTTATGCCTCTGAGAGCTCT
GCTACATAAAGTGGAAGACACGCTAGAGATTCTGGAATTAGAGGGGTGTAGAATGATTGACTCACAACTCAATGCCCCCC
TTCCTGCCCTCAGACAATGCTCTCAGCTCACCAAGATCAACCTCTACAAAAATGACTTCTCCATGCACATCCTAAGGGCC
CTTTTGCAGCACACAGCCAACTGGAACAAGATCGTTGTAGAACAATACCCTGCTCCTCTGGAGTGCTATGATGAGTTGTC
ACATGTCTCCAGAGAAAGATTTTCACAACTATGTTCTCAGCTAATGGCTACACTCAGGACAATAAGGCAGCCCAAGAACA
TCACCTTTCTTACAAAAATGTGCCAAACATGTGCCAAGCACTGTGTCTATACCCAGGTGACCAGACTTTGCAGGTGCTGG
CATTAA

Alignment

ORF - retro_rnor_396 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.38 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFQTPPTLQKLARQTLLRNEAVAMSCVGELPIVLFPALFKEAFEGRHINLVKEMVAAWPFPCLPVGALM
          MS.QTPPTLQ.L....LLRNEA.AMS..GELP.VLFP..FKEAF..RH.NLVKEMVA..PFPCLPVGALM
Retrocopy MSVQTPPTLQELTVHSLLRNEAMAMSYLGELPAVLFPKVFKEAFARRHNNLVKEMVAVLPFPCLPVGALM

Parental  KTPNAETLQAVLDGVDMRLTRKFHPRRIKLQVLDLRNVKHAFWNTWTGAEDCSCSAENLEEKQVVKVFPR
          ..PN..T.QA.LDG.DM.L...FH.R...L..LDLRNV.HAFWN...G....SCS.E.L..KQVVKVFPR
Retrocopy EIPNLKTYQALLDGIDMGLKEEFHHREKNLKILDLRNVHHAFWNICAGEGKSSCSSETLDKKQVVKVFPR

Parental  YALRRQRVKVITELSIFSCLEEQQACFLKWAQERMGSLYFCCTKMKIWDLPVCVIREILNVFDPQHITEL
          Y.LR.QR..VI..L.....L.E.QA.FL.W.Q.R..SLYFC..KM.IW.LP...I..ILNVFD..HITEL
Retrocopy YVLR-QRLRVIVDLCLKLSLNEAQAYFLSWVQQRKSSLYFCYIKMTIWSLPFQDIKGILNVFDTEHITEL

Parental  ELHTEWTLLELEHFAPYFGQMRNLRKVFLEPFHKVTLSNRNETRDREAKCIKKFISQFSKFNCLQHLCMF
          ELHT.WTLL.L..FA.YFGQMRNLRK..L.P.H..T.S....T..RE......FISQFS.FNCLQHL...
Retrocopy ELHTKWTLLQLGYFAHYFGQMRNLRKLILAPLHMRTFSTVERTMVRETRSVNNFISQFSQFNCLQHLFIS

Parental  CTHFLRDHMNQVLGCLMTPLETLSVTCCVISQNDLDSFSCCLSLFHLKHLDLRGVVLHDLDVMPLRVLLE
          ..HFLR..MNQ.LGCLMT.LETLSVT..V.SQ..L.SF.CC.SLF.LKHLDLR..VL..LD.MPLR.LL.
Retrocopy QVHFLRVQMNQILGCLMTRLETLSVTNYVTSQGNLNSFACCQSLFQLKHLDLRETVLYSLDLMPLRALLH

Parental  KVADTLETLDLQWCRMKNSQLYALLPALRHCSQLTTVKFYSNKFSMPILKDLLQHTANWSKVNVEQYPAP
          KV.DTLE.L.L..CRM..SQL.A.LPALR.CSQLT....Y.N.FSM.IL..LLQHTANW.K..VEQYPAP
Retrocopy KVEDTLEILELEGCRMIDSQLNAPLPALRQCSQLTKINLYKNDFSMHILRALLQHTANWNKIVVEQYPAP

Parental  QECYDDSSQVSVERFSQLCHELMDTHRAIRQPKNISFATEICYTCGERCVYHNGPRLCCC
          .ECYD..S.VS.ERFSQLC..LM.T.R.IRQPKNI.F.T..C.TC...CVY....RLC.C
Retrocopy LECYDELSHVSRERFSQLCSQLMATLRTIRQPKNITFLTKMCQTCAKHCVYTQVTRLCRC

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	0.00 RPM	0.07 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_396 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013324	1 retrocopy	retro_dord_231,
Homo sapiens	ENSG00000187545	1 retrocopy	retro_hsap_220,
Otolemur garnettii	ENSOGAG00000000273	2 retrocopies	retro_ogar_1100, retro_ogar_1238,
Ochotona princeps	ENSOPRG00000009716	1 retrocopy	retro_opri_661,
Pan troglodytes	ENSPTRG00000029629	1 retrocopy	retro_ptro_330,
Rattus norvegicus	ENSRNOG00000042820	1 retrocopy	retro_rnor_1371,
Rattus norvegicus	ENSRNOG00000048835	1 retrocopy	retro_rnor_396 ,