RetrogeneDB ID: retro_rnor_1277

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:62576802..62577779(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ddx5
• Ensembl ID: ENSRNOG00000030680
• Aliases: None
• Description: probable ATP-dependent RNA helicase DDX5 [Source:RefSeq peptide;Acc:NP_001007614]

Sequence

>retro_rnor_1277
AGACAGCTCGCTAAAGATTTCCTGAAAGTCTACATTCATATCAATACTGATACACTGGAACTGAGTGCAAACCATAACAT
TCTTCAGATTGTCGATGTGTATCACGATGTCAAAAAGAATGGAAAAAACTTATTCATCTGATGGAAAAGAGCATGAATTA
CAAGGAGAATAAAAACATCATTTTTGTTAAAATCAAAAGAAGATGTGATGAACTTACCAGAAAACTGGGGAGAGATGGGT
GGGCTGCCATGGGCATCCATGGTGACAAGAGTCAGCAGGAATGTGACTGGCTTCTAAATAAATTCAAACATGGAAAAGTT
CCTATTCTAATTGCTACTGATGTGACCTCCTGAGGGCTAGATGTGGAAAATGTAAAATTTGTCATCAATTATGACCACTC
TAACTCCTCAGAGGATTATGTTCATCGAATTGGAAGAACTGCTCACAGTACCAAAACAGACACTGCATACATTTTCTTTA
TACCCAATAACATAAAGCAGGTAAACAACCTCATCTCTGTGCTTCAGGAAGCTAATCCAGCAATTAATCCCAAGTTGCTA
TAGTTATTCGAAGACAGAGATTCGGGTCATTCCAGGGGTAGAGGAGGCATGAAGGATGATCATCACAACAGATACTCTGC
AGGCAAAGGGGGTGGATTTAATACCTTTAGAGACAGAGAAAACTGTAACAGAGCCTACCCTAGTCAGCTTAAAAGAGATT
TGAGGGCTAAGACTCAGAATGGTGTTCACAGTGCTCCAAATTACACCAATGGAAGCTTTGGAAGAAATTTTGTATCACCT
GGTATACAGACCAGTTGTAGGACTGGTAATTCAACAGGGACTTACCAGAATGGTTATGATAGCACTTAGCTATATGGAAA
TAATGTTGCAAGTATGCACAATGGTATGAACCAACAAGAATATATATTTTCTGCTACCGTAGCTGTTGCACCTATGACTG
GCTGTCCAATGCCAACA

Alignment

ORF - retro_rnor_1277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 52.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDV-EKD-EKLIRLMEEIMSEKENKTIVFVETKRRC
          RQLA.DFLK.YIHIN...LELSANHNILQIVDV.HDV..K...KLI.LME..M..KENK.I.FV..KRRC
Retrocopy RQLAKDFLKVYIHINTDTLELSANHNILQIVDVYHDV<QKEWKKLIHLMEKSMNYKENKNIIFVKIKRRC

Parental  DELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSSED
          DELTRK..RDGW.AMGIHGDKSQQE.DW.LN.FKHGK.PILIATDV.S.GLDVE.VKFVINYD..NSSED
Retrocopy DELTRKLGRDGWAAMGIHGDKSQQECDWLLNKFKHGKVPILIATDVTS*GLDVENVKFVINYDHSNSSED

Parental  YIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMKDDRR
          Y.HRIGRTA.STKT.TAY.FF.PNNIKQV..LISVL.EAN.AINPKLL.L.EDR.SG.SRGRGGMKDD..
Retrocopy YVHRIGRTAHSTKTDTAYIFFIPNNIKQVNNLISVLQEANPAINPKLL*LFEDRDSGHSRGRGGMKDDHH

Parental  DRYSAGKRGGFNTFRDRENYDRGYSSLLKRDFGAKTQNGVYSAANYTNGSFGSNFVSAGIQTSFRTGNPT
          .RYSAGK.GGFNTFRDREN..R.Y.S.LKRD..AKTQNGV.SA.NYTNGSFG.NFVS.GIQTS.RTGN.T
Retrocopy NRYSAGKGGGFNTFRDRENCNRAYPSQLKRDLRAKTQNGVHSAPNYTNGSFGRNFVSPGIQTSCRTGNST

Parental  GTYQNGYDSTQQYGSNVANMHNGMNQQAYAYPATAAAAPMIGYPMPT
          GTYQNGYDST..YG.NVA.MHNGMNQQ.Y...AT.A.APM.G.PMPT
Retrocopy GTYQNGYDST*LYGNNVASMHNGMNQQEYIFSATVAVAPMTGCPMPT

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	475.16 RPM
SRP017611_kidney	0.00 RPM	658.95 RPM
SRP017611_liver	0.00 RPM	396.23 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1277 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000013691	1 retrocopy	retro_rnor_1276,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277 ,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,