RetrogeneDB ID: retro_rnor_2937

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:68966899..68967307(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dctd
• Ensembl ID: ENSRNOG00000013215
• Aliases: None
• Description: Deoxycytidylate deaminase [Source:UniProtKB/Swiss-Prot;Acc:Q5M9G0]

Sequence

>retro_rnor_2937
AATACAGAGAACAAGATTCTTGGGATTCCGATACAGTGGAATGCCAAATGGGTTCAGTGAGGACTTGTTGCCTTGGAGGA
GAACAGCAGAAAATAAGCTGGCACTGAAGATCTTTATGAGTGTCATTCGAAGCTGAATACCACCAGGAACAAAAATTCAG
CTGATATGAAGGACTATAATATGCTCATTGCCTTGATCCTGTGTGGTGAATGTGCTGAGTTCATCATTCAGGAAGGTATT
CAAGAAGTTATTTTCATGTCAGATAAATATCCCGGCAGTGAATAGACAATGGGCATTAGGCTCATGTTTAAATTGCCCGG
AGTTACAGTCAGAAAATTCACACTGAAATACAGCAAGATTTTCATTGACTCCGATTCAATTAATAGCTGACTGAGTCAGA
AGCCCCAG

Alignment

ORF - retro_rnor_2937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.12 %
• Parental protein coverage: 73.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NTENKIVGIG-YNGMPNGCSDDLLPWRRTAENKL-DTKYPYVCHAELNAIMNKNSADVKGCSMYVALFPC
          NTENKI.GI..Y.GMPNG.S.DLLPWRRTAENKL..T...Y.CH..LN...NKNSAD.K...M..AL..C
Retrocopy NTENKILGIP>YSGMPNGFSEDLLPWRRTAENKL<GTEDLYECHSKLNTTRNKNSADMKDYNMLIALILC

Parental  NECAKLIIQAGIKEVIFMSDKYHDSEETTAARLLFKLAGVTFRKFTPKYSKIVIDFDSINSRPSQKPQ
          .ECA..IIQ.GI.EVIFMSDKY..SE.T...RL.FKL.GVT.RKFT.KYSKI.ID.DSINS..SQKPQ
Retrocopy GECAEFIIQEGIQEVIFMSDKYPGSE*TMGIRLMFKLPGVTVRKFTLKYSKIFIDSDSINS*LSQKPQ

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	4.96 RPM
SRP017611_kidney	0.00 RPM	7.89 RPM
SRP017611_liver	0.00 RPM	1.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2937 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2937 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017516	3 retrocopies	retro_ecab_829, retro_ecab_830, retro_ecab_915,
Mus musculus	ENSMUSG00000031562	1 retrocopy	retro_mmus_3672,
Rattus norvegicus	ENSRNOG00000013215	1 retrocopy	retro_rnor_2937 ,
Sarcophilus harrisii	ENSSHAG00000015218	1 retrocopy	retro_shar_124,
Tursiops truncatus	ENSTTRG00000001460	1 retrocopy	retro_ttru_613,