RetrogeneDB ID: retro_ocun_1185

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:22609192..22610087(-)
• Located in intron of: ENSOCUG00000015943

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016174
• Aliases: None
• Description: None

Sequence

>retro_ocun_1185
GCAGCGATGGCGGCAGCAGCTGGGGCTGCAGGTGGTCAGGGCTCCGGGCCAGGGCGGGGGCGCCATCTTATGCCCGGGGC
CAGTGGGGAGGCCGGAGAGGGGGCCCCAGGGGGCGCAGGGGACTACGGAAACGGCCTGGAGTCTGAGGAACTAGAGCCTG
AGGAGCTGCTGCCAGAGCCCCAGCCCAAAGAGGAGCTGCCCCAGCCCCGCACACCCCGGGAACTCCGGGCCTTGGGCCTG
GCTCGGGAGCCTCCGGCAACCAGGAGGAGGAGGAGGAGCCGGGACTGGTGGAGGGTGACCCGGGGGACAGCGCCATTGAG
GACCCAGATCTGAAAGCAATCAAAAGCCCGAGTCATGGAGATGGAGGAGGAAGCTAAGAAGCTAAAAGAGCTGCAGAACG
AGGTAGAGAAGCAGATGAGTATGAGTCCACCTCCAGGCAGTGTTGGCCCAGTGATCATGTCTATTGAGGAGAGGATGGAG
GCTGACGCCCGTTCCATCTATATTAGCAATGTGGACTATGGTGCAACCGCAGAAGAGCTGGAAGCTCACTTTCATGGCTG
TGGTTCTGTCAACCGTGTGACGATACTCTGTGACAAGTTCAGTGGCCATCCCAAAGGGTTTGCATATATAGAGTTCTCAG
ATAAAGAGTCAGTGAGAACTTCCCTGGCCTTAGATGAGTCCCTATTTAGAGGAAGACAAATCAAGGTGATTCCAAAACGA
ACCAACAGACCAGGCATCAGCACAAACAGACCGGGGTTTCCCACATGCCCGCTACCGTGCCAGGACCACCAACTACAACA
GTTCCCGCTCTAGATTCTACAGTGGTTTTAACAGCAGGCCCCGGGGTCACATCTACAGGGGCCAGGCTAGAGCGACATCA
TGGTATTCCCGTTAC

Alignment

ORF - retro_ocun_1185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.37 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGAPGGAGDYGNGLESEELEPGELLPEPEPEEEPPRPR
          AA.AAAAGAAGG.GSGPGR.RHL.PGA.GEAGEGAPGGAGDYGNGLESEELEP.ELLPEP.P.EE.P.PR
Retrocopy AAMAAAAGAAGGQGSGPGRGRHLMPGASGEAGEGAPGGAGDYGNGLESEELEPEELLPEPQPKEELPQPR

Parental  AP-PGTPGPGPGSGAPGNQEEEEEPGLVEGDPGDSAIEDPELEAI-KARVREMEEEAEKLKELQNEVEKQ
          .P.PGTPG.GPGSGA.GNQEEEEEPGLVEGDPGDSAIEDP.L.AI.KARV.EMEEEA.KLKELQNEVEKQ
Retrocopy TP<PGTPGLGPGSGASGNQEEEEEPGLVEGDPGDSAIEDPDLKAI>KARVMEMEEEAKKLKELQNEVEKQ

Parental  MNMSPPPGNAGPVIMSIEERMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFA
          M.MSPPPG..GPVIMSIEERMEADARSIY..NVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFA
Retrocopy MSMSPPPGSVGPVIMSIEERMEADARSIYISNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFA

Parental  YIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGIST-TDRGFPRARYRARTTNYNSSRSRFYSGFN
          YIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGIST.TDRGFP.ARYRARTTNYNSSRSRFYSGFN
Retrocopy YIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGIST>TDRGFPHARYRARTTNYNSSRSRFYSGFN

Parental  SRPRGRIYRGRARATSWYSPY
          SRPRG.IYRG.ARATSWYS.Y
Retrocopy SRPRGHIYRGQARATSWYSRY

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	94.37 RPM
SRP017611_kidney	0.00 RPM	57.77 RPM
SRP017611_liver	0.23 RPM	42.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1185 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1185 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Oryctolagus cuniculus	ENSOCUG00000016174	4 retrocopies	retro_ocun_1185 , retro_ocun_1741, retro_ocun_1930, retro_ocun_365,