RetrogeneDB ID: retro_ocun_804

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:57700817..57701181(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024708
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFDN1
• Ensembl ID: ENSOCUG00000009432
• Aliases: None
• Description: prefoldin subunit 1 [Source:HGNC Symbol;Acc:8866]

Sequence

>retro_ocun_804
ATGGCTGCCCCTGTGGATCTCGAGTTGAAGAAGGCCTTCACAGAGCCTCAAGCCAAAGTTATTGCCACTCAACAGAAGGC
GAAGCTTGCTGACATACAGATTGAGCAACTGAACAGAACAAAAAAAAATGCACATCTTACAGATACAGAAATTAGGACTT
TGGTAGATGAGACTAACATGTATGAAAGTGTGGGGAGAATGTTTATTCTTTATTCCAAGGGGGTAATTCACAATCAATGG
TTTGATAAACAGAATATAGCAGAAGAAAAAAGTAAAGAACTAGAGCAGAGAAAAATCCTAAATAGAGCAGAGCTTTAAGG
ATGCAGAAGACAACGTCTAGGAAATGATATTGGCAAGAAGGTCA

Alignment

ORF - retro_ocun_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPVDLELKKAFTELQAKVIDTQQKVKLADIQIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFIL
          MAAPVDLELKKAFTE.QAKVI.TQQK.KLADIQIEQLNRTKK.AHLTDTEI.TLVDETNMYE.VGRMFIL
Retrocopy MAAPVDLELKKAFTEPQAKVIATQQKAKLADIQIEQLNRTKKNAHLTDTEIRTLVDETNMYESVGRMFIL

Parental  QSKEVIHNQLLEKQKIAEEKIKELEQK-KSYLERSVKEAEDNIREMLMARRA
          .SK.VIHNQ...KQ.IAEEK.KELEQ..KS..E.S.K.AEDN..EM..ARR.
Retrocopy YSKGVIHNQWFDKQNIAEEKSKELEQR>KS*IEQSFKDAEDNV*EMILARRS

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	32.95 RPM
SRP017611_kidney	0.00 RPM	32.03 RPM
SRP017611_liver	0.00 RPM	7.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_804 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_804 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893, retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629,
Felis catus	ENSFCAG00000001272	1 retrocopy	retro_fcat_1323,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Microcebus murinus	ENSMICG00000000349	1 retrocopy	retro_mmur_1121,
Oryctolagus cuniculus	ENSOCUG00000009432	4 retrocopies	retro_ocun_1049, retro_ocun_1885, retro_ocun_804 , retro_ocun_999,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,
Rattus norvegicus	ENSRNOG00000018653	1 retrocopy	retro_rnor_985,