RetrogeneDB ID: retro_ocun_1385

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:153862058..153862532(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NIPSNAP3A
• Ensembl ID: ENSOCUG00000007880
• Aliases: None
• Description: nipsnap homolog 3A (C. elegans) [Source:HGNC Symbol;Acc:23619]

Sequence

>retro_ocun_1385
GCATCTCAGGTGTGCTCATCTTTTGCTATAGACCCCAGACAAAACCATGCGAAGGTCTATGAATTTGCTACCTATTATCC
TAAACCCTCAAAGATGAATGAGTTCCTTGAAAATTTTACGGAAAACGTTCATCTTTGGACAGCACACTCTGAATTGGTTG
ACTATTGCAGTGTAGAATTTGGTGCAGAATGAATGAAGTGTTTCATATTTGGAAGTAGGATAATCTTGCTTATCGAACTG
AAGTTCATAAAGCTTTGGCCAAAGGAAAGAATGGCAAGAGCAGCCTTTCATTCCAGATTTGCCTCTTGTGGATAAACAAG
AGAGTGAAATTCCTTATCTGGTAATGGAAAAGCCTCCAAAAGAAGGCGTCTATGAACTGGCTACTTTTCAGATGAAACCA
GGTGGCCCAGCCCTGTGGGGTCATGCATTTCAAAGAGCATTCAATGCCCATGTTGCTCAGGATACACAAAGCTA

Alignment

ORF - retro_ocun_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 65.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APQVCSSFATGPRQKDGTFYEFRTYSLKPSKMNEFLENFKKNVHLRTAHSELVGYWRVEFGG-RMNKVFH
          A.QVCSSFA..PRQ.....YEF.TY..KPSKMNEFLENF..NVHL.TAHSELV.Y..VEFG..RMN.VFH
Retrocopy ASQVCSSFAIDPRQNHAKVYEFATYYPKPSKMNEFLENFTENVHLWTAHSELVDYCSVEFGA<RMNEVFH

Parental  IWKYDNFAHRTEVRKALAKD-KEWQEQFLIPNLPLVDKQESEITYLVPWCKLEKPPKEGVYELATFQMKP
          IWK.DN.A.RTEV.KALAK..KEWQEQ..IP.LPLVDKQESEI.YLV.....EKPPKEGVYELATFQMKP
Retrocopy IWK*DNLAYRTEVHKALAKG<KEWQEQPFIPDLPLVDKQESEIPYLV----MEKPPKEGVYELATFQMKP

Parental  GGPALWGDAFKRAVNAHVA-LGYTKL
          GGPALWG.AF.RA.NAHVA..GYTKL
Retrocopy GGPALWGHAFQRAFNAHVA<SGYTKL

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	20.92 RPM
SRP017611_kidney	0.00 RPM	62.84 RPM
SRP017611_liver	0.00 RPM	31.83 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1385 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1385 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133,
Canis familiaris	ENSCAFG00000023949	1 retrocopy	retro_cfam_295,
Cavia porcellus	ENSCPOG00000009373	1 retrocopy	retro_cpor_690,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Myotis lucifugus	ENSMLUG00000010147	1 retrocopy	retro_mluc_924,
Oryctolagus cuniculus	ENSOCUG00000007880	1 retrocopy	retro_ocun_1385 ,
Tursiops truncatus	ENSTTRG00000012307	1 retrocopy	retro_ttru_1702,