RetrogeneDB ID: retro_rnor_1381

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:2266802..2268285(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sdad1
• Ensembl ID: ENSRNOG00000022229
• Aliases: None
• Description: None

Sequence

>retro_rnor_1381
TCTGTCTGGAATGATGTCAAAGCAGTCAATGTTATCACAACCACATGTTTCTCCAAGATCACCAAGATATTAGTTGCTGC
TGTGATGTTCTTCCTCAGGAAAGATGAGGAAGAGAAGCAAGACAGTGACTCAGAATCTGGGGACGACAGGCCCACAGCGA
GAGACCTGCTGGGGCAATATGCCACGGGAAAGGAGGGCTCCAAAACCAAGAAGCTGGAAAAGGTCGTGGAAGTGCTGAAG
AAACAAAAGAAGAAAAGGAAACCAGAAGTGTTTAACTTTTCAGCTATTCACTTGATTCATGATCCCCAAGACTTTGCAGA
AAAGTTTCTGAGGCAGCTAGAGAGCTGTAAGGAGAGGTTTGAAGTGAAGATGATGCTCACACACCTCATCTCCAGATTGA
TGGGGATTCACGAGCTTTTCCTCTTCCACTTCTACCCTTTTGTGCAAAGGTTTCTGCAGCCCCACCAGAGAGAAGTCACA
AAGATCCTTCTGTTTGCCAACAAGCCTCTCATCACCTGGTGTCCCCAGAAATTATTCAGCCATTGCTCATGACAGTGGCC
AACAATTTTGTTACTGACAAGAACTCTGGGGAAGTTATGACTGTAGGAATCAATGCTATAAAAGAAATCACAGCTCGATG
TCCTCTGGCCATGGCTGAAGAACTTCTTCAGGACCTGGCTAAGTATAAGACACACAAAGATAAGAACATAATGATGCCTA
CCAGAACTTTGATCCATCTCTTCAGACACCGAATCCTCAGATGTTGCAGAAGAAGTTCCAGGGTAAATCCACCTAAGCCT
CCATCAAAGCAAGAATACAAGAATATAGAGAATTAGATGCTAAAGATTACATCCCAGGAGCAGGGGTTCTAGAACTTGAG
GAAGAAGAGGATACAGAAAATGGTGAAGATGGATGGGAAAGTGCCATCCTCAGTGAGGAGGAGGAGGATGGTGAGTGGGT
TGATGTGCACCATTCTTCTGACAAGGAGCAGCAAGCAATTGCCAAGAGTTGGACAGCATGTCCATGGAGGAGTGGAAGGA
CAAATCTGCAGCCATCAGCACCAGTGGGGTTTTAACGTAGGATGGCGTCCAGACACTCCGCATGGCCCACATGAAGAAGG
AAATGGATGCTGCCCAGTGAAAGCCCAGAGAGCGAAATACTTGGAAACTGACAGTGATGAGGAGTCCAGGGGGAAATTAC
TGTCTCTTTGGGACATTGAACACCTTCATAAAAAGCCCGTCTGACAAGGAGATGAGACTAACGACCACAATGGCTGGAAG
GACAGACCGAAAGGAGTTTGTGAGGCAGAAAACCAAAACAAACCCAGTTTCCAGTTCCACAAATAAAGAGAAGAAAAAGC
AGAAGAACTTTATGATGACACAGTATAGATAGTCAGAATGTCTAGTCAAGAACAGCACGCTCCTTCTGGGAGAAGCAGCT
GGCACTGTGAGATGCGCCTCTGAAAAAGAGGAAAAGAATGAAG

Alignment

ORF - retro_rnor_1381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.72 %
• Parental protein coverage: 72.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NIWNDAKTVNVITTACFSKITKILVAALTFFLGKDEEEKQDSDSESEDDGPTARDLLVQYATGKKGSKNK
          ..WND.K.VNVITT.CFSKITKILVAA..FFL.KDEEEKQDSDSES.DD.PTARDLL.QYATGK.GSK.K
Retrocopy SVWNDVKAVNVITTTCFSKITKILVAAVMFFLRKDEEEKQDSDSESGDDRPTARDLLGQYATGKEGSKTK

Parental  KKLEKAMKVLKKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLESCKERFEVKMMLMNLISRLVGIHEL
          K.LEK...VLKKQKKK.KPEVFNFSAIHLIHDPQDFAEK.L.QLESCKERFEVKMML..LISRL.GIHEL
Retrocopy K-LEKVVEVLKKQKKKRKPEVFNFSAIHLIHDPQDFAEKFLRQLESCKERFEVKMMLTHLISRLMGIHEL

Parental  FLFNFYPFVQRFLQPHQREVTKILLFA-AQASHHLVPPEIIQSLLLTVANNFVTDKNSGEVMTVGINAIK
          FLF.FYPFVQRFLQPHQREVTKILLFA..QASHHLV.PEIIQ.LL.TVANNFVTDKNSGEVMTVGINAIK
Retrocopy FLFHFYPFVQRFLQPHQREVTKILLFA<QQASHHLVSPEIIQPLLMTVANNFVTDKNSGEVMTVGINAIK

Parental  EITARCPLAMTEELLQDLAQYKTHKDKNVMMSARTLIHLFR-TLNPQMLQKKFRGKPTEASIEARIQEYG
          EITARCPLAM.EELLQDLA.YKTHKDKN.MM..RTLIHLFR.T.NPQMLQKKF.GK.T.ASI.ARIQEY.
Retrocopy EITARCPLAMAEELLQDLAKYKTHKDKNIMMPTRTLIHLFR<TPNPQMLQKKFQGKST*ASIKARIQEYR

Parental  ELDAKDYIPGAEVLELEKEENTENDEDGWESASLSEEEEDGEWVDVHHSSDEEQQAVAK-KLDSMPMEER
          ELDAKDYIPGA.VLELE.EE.TEN.EDGWESA.LSEEEEDGEWVDVHHSSD.EQQA.AK..LDSM.MEE.
Retrocopy ELDAKDYIPGAGVLELEEEEDTENGEDGWESAILSEEEEDGEWVDVHHSSDKEQQAIAK<ELDSMSMEEW

Parental  KAKAAAVSTSRVLTQDDFQKIRMAQMKKEMDAA-PGKAQKRKYLDMDSDEESRGELLSLRDIERLH-KKP
          K.K.AA.STS.VLT.D..Q..RMA.MKKEMDAA.P.KAQ..KYL..DSDEESRG.LLSL.DIE.LH.K.P
Retrocopy KDKSAAISTSGVLT*DGVQTLRMAHMKKEMDAA<PVKAQRAKYLETDSDEESRGKLLSLWDIEHLH>KSP

Parental  KSDKETRLATAMAGRTDRKEFVRKKTKINPFSSSTNKE-KKKQKNFMMMRY-SQNVRSKTSRSFREKQLA
          .SDKE.RL.T.MAGRTDRKEFVR.KTK.NP.SSSTNKE.KK.....M.....SQNV.S.T.RSF.EKQLA
Retrocopy -SDKEMRLTTTMAGRTDRKEFVRQKTKTNPVSSSTNKEKKKQKNFMMTQYR>SQNV*SRTARSFWEKQLA

Parental  LRDALLKKRKRMK
          L.DA.LKKRKRMK
Retrocopy L*DAPLKKRKRMK

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	10.64 RPM
SRP017611_kidney	0.07 RPM	11.51 RPM
SRP017611_liver	0.00 RPM	5.11 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1381 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1381 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1381 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515,
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946, retro_etel_779,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381 , retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,