RetrogeneDB ID: retro_ocun_691

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:45480933..45481659(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025667
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSOCUG00000013592
• Aliases: None
• Description: RWD domain containing 1 [Source:HGNC Symbol;Acc:20993]

Sequence

>retro_ocun_691
ATGACAGATTACCGCGAGGAACAGCGTAAGGAGCTGGAGGCCCTGGAATCCATCTACACTGACTCCTTCACAGTATTATC
AGAAAAGCCACCCAGCTTCACCATTACTGTGACATCTGAGGCAGGAGAGAAAGATGAAACTGTCCAGACTACCCTCAAGT
TTACACACAGTGAAAAATACCCAGATGACATTCCTCTTTATGAAATATTCTCCCAGGAAAATCTAGAAGATAATGATGTA
TCAGACATTTTAAAATTATTAGCATTACAGGCTGAAGAAAATCTTGGCATGGTGATGATCTTTACTCTAGTGACAGCTGT
GCAAGAAAAATTAAATGAAATAGTAGATCAGATAAAAACTAGAAGAGAGGAAGAAAAGAAACAAAAGAAAAAAGAAGCCG
AAGAAGCTGAAAAGCAAATATTCCATGGCGCACCTATTACAATTGAGAATTTCTTAAGTTGGAAGGCCAAGTTTGATGCA
GAACTCTTGGAAATTAAAAAGAAACGAATGAAAGAAGAAGAACAAGCAGGAAAAAATAAATCAAGTGGGAAACAGCTGTT
TGAAACAGATCATAATCTTGACACATCTGATATCCAGTTCTTGGAGGATGCTGGCAACAGTGTGGAAGTAGATGAGTCTT
TGTTCCAGGAAATGGGTGACTTGGAGCTGGAGGATGATGATGATGATCCAGACCTCAATCCTGCTGACCCAGGAAGTGAC
TCAACC

Alignment

ORF - retro_ocun_691 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.02 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDYGEEQRNELEALESIYPDSFTVLSEKPPSFTITVTSEAGENDETVQTTLKFTYSEKYPDETPLYEIF
          MTDY.EEQR.ELEALESIY.DSFTVLSEKPPSFTITVTSEAGE.DETVQTTLKFT.SEKYPD..PLYEIF
Retrocopy MTDYREEQRKELEALESIYTDSFTVLSEKPPSFTITVTSEAGEKDETVQTTLKFTHSEKYPDDIPLYEIF

Parental  SQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKIIFLEIRKMNKTMSDSYQKQL
          SQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIK....E..K..K.......KQ.
Retrocopy SQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKTRREEEKKQKKKEAEEAEKQI

Parental  FHGTPVTIENFLSWKAKFDAELLEIKKKRMKEEEQAGKNKLSGKQLFETDHNLDTSDIQFLEDAGNNVEV
          FHG.P.TIENFLSWKAKFDAELLEIKKKRMKEEEQAGKNK.SGKQLFETDHNLDTSDIQFLEDAGN.VEV
Retrocopy FHGAPITIENFLSWKAKFDAELLEIKKKRMKEEEQAGKNKSSGKQLFETDHNLDTSDIQFLEDAGNSVEV

Parental  DESLFQEMDDLELEDDDDDPDYNPADPGSDST
          DESLFQEM.DLELEDDDDDPD.NPADPGSDST
Retrocopy DESLFQEMGDLELEDDDDDPDLNPADPGSDST

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	0.17 RPM	38.19 RPM
SRP017611_kidney	0.61 RPM	40.14 RPM
SRP017611_liver	0.15 RPM	13.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_691 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_691 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_691 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Dasypus novemcinctus	ENSDNOG00000007516	1 retrocopy	retro_dnov_2467,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691 ,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,