RetrogeneDB ID: retro_rnor_1672

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:209548218..209548701(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000011472
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nudt5
• Ensembl ID: ENSRNOG00000017741
• Aliases: None
• Description: ADP-sugar pyrophosphatase [Source:UniProtKB/Swiss-Prot;Acc:Q6AY63]

Sequence

>retro_rnor_1672
ATGGAGGCCAAAGAATCAAAAGACTCTTCTCCTCCCACCAAGTAACGCATTATTTCAGAGGAGTTGAGCTCAGAAGGAAA
ATGGGTCAAATTTGAAAAAACAACTTACATGGACCCCACCAGTAAAACTAGAACCTGGCAAAAAGTGAAACTTAGAACCA
GAAAGGGAAAATCTGCTGAGGCCCTGTCAATCATACCAGTCCTGCAAAGTATGCTTCATCATGAGTGCATTGTTCTGGTG
AAGCAGTTCTGGCCCCTGATAGGCGTCTACTGCCTGGAGTTTCCAGCAGGGCTCATCAAAGATCAGGAAAGCCCAGAAGC
GACTGCTCTTCGGGAGCTGGAGGAAGAAACTGGTTACAAAGGTGATGTTGCCGAATGCTCTCTAGCTGTGTGTATGGATG
CAGGCCTCCCAAACTGCACCACGCATGTTGTGACAGTAACCATCAACGGAGATAATGCAGTAAATGTAAGGCCAAAACCC
AAA

Alignment

ORF - retro_rnor_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 73.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METQEPKDSSPPTEQRILSEELISEGKWVKFEKTTYMDPTGKTRTWETVKLTTRKGKSADAVSVIPVLQR
          ME..E.KDSSPPT..RI.SEEL.SEGKWVKFEKTTYMDPT.KTRTW..VKL.TRKGKSA.A.S.IPVLQ.
Retrocopy MEAKESKDSSPPTK*RIISEELSSEGKWVKFEKTTYMDPTSKTRTWQKVKLRTRKGKSAEALSIIPVLQS

Parental  TLHHECIVLVKQFRPPMGGYCLEFPAGLIEDGESPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCT
          .LHHECIVLVKQF.P..G.YCLEFPAGLI.D.ESPEA.ALRELEEETGYKGD.AECS.AVCMD.GL.NCT
Retrocopy MLHHECIVLVKQFWPLIGVYCLEFPAGLIKDQESPEATALRELEEETGYKGDVAECSLAVCMDAGLPNCT

Parental  THVVTVTINGDDAGNVRPKPK
          THVVTVTINGD.A.NVRPKPK
Retrocopy THVVTVTINGDNAVNVRPKPK

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	5.90 RPM
SRP017611_kidney	0.00 RPM	17.38 RPM
SRP017611_liver	0.00 RPM	9.68 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1672 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1672 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672 ,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,