RetrogeneDB ID: retro_ocun_1945

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:88351473..88351834(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023605
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDZD11
• Ensembl ID: ENSOCUG00000017101
• Aliases: None
• Description: PDZ domain containing 11 [Source:HGNC Symbol;Acc:28034]

Sequence

>retro_ocun_1945
ATGGACAGCCAGATTCCTTATGCTGACTACCTAGTGGTTCTCCTGCCTGCCTATGAGAATCCCCCAGCATGGAGTCACCT
CACCAGAGAGTACACCACCCAGCTACAACAATGAGCTGAGCCAGTTTCTGCCCCGAATCGTCACACTGAGGAAGCCTCCT
GGAGTGGGGCTGGGATTTAACATCCGAGGAGGAGAGGCCTCACAGCCAGGCATCTTCATCTGCAAGGTGATTCCTGACTC
CGACGCACGTCAAGCAGGACTTCAGGATGCCGACCGAGTACTAGCTATGGATAACGTGCATTTGCAAGCTACTGAGCACA
GCAAGGCTGTGGAGATACTGAAGACAGCCCGTGAAATCAGT

Alignment

ORF - retro_ocun_1945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 86.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDSRIPYDDYPVVFLPAYENPPAWI-PPHERVYHP-DYNNELTQFLPRVVTLKKPPGAQLGFNIRGGKAS
          MDS.IPY.DY.VV.LPAYENPPAW...PH.RV.HP..YNNEL.QFLPR.VTL.KPPG..LGFNIRGG.AS
Retrocopy MDSQIPYADYLVVLLPAYENPPAWS<SPHQRVHHP<SYNNELSQFLPRIVTLRKPPGVGLGFNIRGGEAS

Parental  QLGIFISKVIPDSDAHRAGLQEGDQVLAVNDVDFQDIEHSKAVEILKTAREIS
          Q.GIFI.KVIPDSDA..AGLQ..D.VLA...V..Q..EHSKAVEILKTAREIS
Retrocopy QPGIFICKVIPDSDARQAGLQDADRVLAMDNVHLQATEHSKAVEILKTAREIS

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	0.06 RPM	37.58 RPM
SRP017611_kidney	0.00 RPM	38.92 RPM
SRP017611_liver	0.00 RPM	8.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1945 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1945 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009203	1 retrocopy	retro_amel_158,
Bos taurus	ENSBTAG00000012860	1 retrocopy	retro_btau_594,
Callithrix jacchus	ENSCJAG00000012432	1 retrocopy	retro_cjac_138,
Cavia porcellus	ENSCPOG00000000210	1 retrocopy	retro_cpor_143,
Echinops telfairi	ENSETEG00000008626	3 retrocopies	retro_etel_1026, retro_etel_1863, retro_etel_921,
Felis catus	ENSFCAG00000008633	3 retrocopies	retro_fcat_1356, retro_fcat_1410, retro_fcat_263,
Homo sapiens	ENSG00000120509	1 retrocopy	retro_hsap_1439,
Gorilla gorilla	ENSGGOG00000006626	1 retrocopy	retro_ggor_1108,
Macropus eugenii	ENSMEUG00000012040	1 retrocopy	retro_meug_1858,
Macaca mulatta	ENSMMUG00000013938	1 retrocopy	retro_mmul_2265,
Nomascus leucogenys	ENSNLEG00000000863	1 retrocopy	retro_nleu_1414,
Oryctolagus cuniculus	ENSOCUG00000017101	2 retrocopies	retro_ocun_1208, retro_ocun_1945 ,
Ochotona princeps	ENSOPRG00000001811	1 retrocopy	retro_opri_374,
Pongo abelii	ENSPPYG00000020929	1 retrocopy	retro_pabe_1193,
Pan troglodytes	ENSPTRG00000021995	1 retrocopy	retro_ptro_981,
Rattus norvegicus	ENSRNOG00000002838	1 retrocopy	retro_rnor_615,
Sarcophilus harrisii	ENSSHAG00000005380	1 retrocopy	retro_shar_149,
Ictidomys tridecemlineatus	ENSSTOG00000027107	2 retrocopies	retro_itri_1264, retro_itri_1702,
Tursiops truncatus	ENSTTRG00000007864	1 retrocopy	retro_ttru_953,