RetrogeneDB ID: retro_rnor_2585

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:90250000..90250410(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000009551
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pafah1b2
• Ensembl ID: ENSRNOG00000018032
• Aliases: None
• Description: Platelet-activating factor acetylhydrolase IB subunit beta [Source:UniProtKB/Swiss-Prot;Acc:O35264]

Sequence

>retro_rnor_2585
ATGAGCCAAGGAGACTCGAACCCAGCAGCTATTCCACATGCAGCAGAAGATATTCAAGGAGGTGACAGCTGGATGTTTCA
GCATAATAGGTTTGTTCTGGACTGTAAAGACAAAGAGCCGGACGTGTTGTTTGTGGGAGACTCCGTGGTACAGTTAATGC
AGCATTACGAGATATGGCGGGAGCTGTTTTCCCCACTTCATGCTCTTAATTTTGGAACTGGGGGAGACACACATGACATG
TTTTATGGACACTAAAAGAGGGAGAGCTGGAGAACATTAAGCCTAAAGCCATTGTTGTCTGGGTAGGAACAAACAACCAT
GAAAATACAGCAGAAGAAGTAGCAGGTGGAATTGAGGCTATTGTACAACTTATAAACACGCGGCAGCCACAGGCCAAGGT
CTGTTACCTC

Alignment

ORF - retro_rnor_2585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 59.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHALN
          MSQGDSNPAAIPHAAEDIQG.D.WM.QHNRFVLDCKDKEPDVLFVGDS.VQLMQ.YEIWRELFSPLHALN
Retrocopy MSQGDSNPAAIPHAAEDIQGGDSWMFQHNRFVLDCKDKEPDVLFVGDSVVQLMQHYEIWRELFSPLHALN

Parental  FGIGGDT-TRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIIVL
          FG.GGDT.T.HVLW.LK.GELENIKPK.IVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAK...L
Retrocopy FGTGGDT<T*HVLWTLKEGELENIKPKAIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKVCYL

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	64.85 RPM
SRP017611_kidney	0.00 RPM	40.19 RPM
SRP017611_liver	0.00 RPM	11.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2585 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2585 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585 ,
Rattus norvegicus	ENSRNOG00000020481	1 retrocopy	retro_rnor_976,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,