RetrogeneDB ID: retro_rnor_2542

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:835805..836179(+)
• Located in intron of: ENSRNOG00000029876

Retrocopy information

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

Parental gene information

• Parental gene symbol: Qdpr
• Ensembl ID: ENSRNOG00000003253
• Aliases: None
• Description: Dihydropteridine reductase [Source:UniProtKB/Swiss-Prot;Acc:P11348]

Sequence

>retro_rnor_2542
CACTTGGTTACAAAGCACCTGAAGGAAGAAGGTCTCTCGACCCTGGCTGGGGGCAAAGCTGCCTTGGTTAGGACTCCTGG
GATGATCATCTATGTCATGGCTAAGAGAGCCATCCATCAGCCTTGCCAGAACCTTGCAGGGAAGAAAAGTGGCATGACAC
CCGGGGCTACCACCATTGCTGTGCTCCCCATTACCCTGGATACTCCGATGGACAAGAAATCAATGCCCAAGGCAGACTTC
AGCTCCTGGACACACTTAGAGGTCCTGGTGGAGACCTTCCATGACTGGATCACTGGGAACAAATGGCCAAACTCAGGAAG
TCTAATCCAAGTGACAACCACAGATGGGAAGACCCGTTTACTCCAGCATATTTT

Alignment

ORF - retro_rnor_2542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 51.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HLATKHLKEGGLLTLAGAKAALDGTPGMIGYGMAKGAVHQLCQSLAGKNSGMPSGAAAIAVLPVTLDTPM
          HL.TKHLKE.GL.TLAG.KAAL..TPGMI.Y.MAK.A.HQ.CQ.LAGK.SGM..GA..IAVLP.TLDTPM
Retrocopy HLVTKHLKEEGLSTLAGGKAALVRTPGMIIYVMAKRAIHQPCQNLAGKKSGMTPGATTIAVLPITLDTPM

Parental  NRKSMPEADFSSWTPLEFLVETFHDWITGNKRPNSGSLIQVVTTDGKTEL-TPAYF
          ..KSMP.ADFSSWT.LE.LVETFHDWITGNK.PNSGSLIQV.TTDGKT.L.TPAYF
Retrocopy DKKSMPKADFSSWTHLEVLVETFHDWITGNKWPNSGSLIQVTTTDGKTRL<TPAYF

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	77.22 RPM
SRP017611_kidney	0.00 RPM	218.49 RPM
SRP017611_liver	0.00 RPM	225.04 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2542 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2542 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000002897	1 retrocopy	retro_meug_462,
Myotis lucifugus	ENSMLUG00000003473	1 retrocopy	retro_mluc_2092,
Monodelphis domestica	ENSMODG00000000879	1 retrocopy	retro_mdom_844,
Rattus norvegicus	ENSRNOG00000003253	1 retrocopy	retro_rnor_2542 ,
Tarsius syrichta	ENSTSYG00000002627	2 retrocopies	retro_tsyr_1237, retro_tsyr_1696,