RetrogeneDB ID: retro_ocun_1698

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018783:494637..495138(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOL12
• Ensembl ID: ENSOCUG00000017013
• Aliases: None
• Description: nucleolar protein 12 [Source:HGNC Symbol;Acc:28585]

Sequence

>retro_ocun_1698
TACCTGTCAGGCTTCCCCAAGCAGAAGGTGGAGCTCAAGAAGGTCGCCATCCAGGAGATTAAGCAGCAGCTGAAGGAGCA
ACAGAAGCAGCTGTGAGAGGAGCGCCACCAGGAATACTTGAAGATGTTGGCAGAGAGAGAGGAGGCACGGGAGGAGGCTG
ATGAGCTGGACCAGCTGGTGACGGCAAAGACAGAGTCAGTGCAGTATGACCACCCCTACCACACAGTCACCGTGGCCACC
ATCAGTGACCTGGATATCTCCGGGATCAGGCTGCTCAGGATGTCACTGCCCAAGCAAGGGCCAGGGGATGAATCCAAGGA
GGAGGCACCACCCATGGAGAAGTCAACCAGAGCCTTACCCAGGAAGTCCAAAGACTCCCTGCTGTCTCAGCAGATTTCCT
CCCTCACAGTGACACTGCATACATACAGCCGCAAGAAGGTCAAGTGGAAACATCCCCAAGGTACCCAGGACTCCAAGAAG
CCCCCAAGTGCCAGGCACACC

Alignment

ORF - retro_ocun_1698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.65 %
• Parental protein coverage: 78.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLTGFHKRKVERKRAAIQELQQRLKEEQRKLREERHQEYLKMLAEREEALEEADELDRLVTAKTESVQYD
          YL.GF.K.KVE.K..AIQE..Q.LKE.Q..L.EERHQEYLKMLAEREEA.EEADELD.LVTAKTESVQYD
Retrocopy YLSGFPKQKVELKKVAIQEIKQQLKEQQKQL*EERHQEYLKMLAEREEAREEADELDQLVTAKTESVQYD

Parental  HPNHTVTVTTISDLDLSGARLLGLSPPEQGPGDESKEEAPSVEKPTRALPRKSKDPLLSQRICSLTATLH
          HP.HTVTV.TISDLD.SG.RLL..S.P.QGPGDESKEEAP..EK.TRALPRKSKD.LLSQ.I.SLT.TLH
Retrocopy HPYHTVTVATISDLDISGIRLLRMSLPKQGPGDESKEEAPPMEKSTRALPRKSKDSLLSQQISSLTVTLH

Parental  AHSRKKVKRKRPRHSQDSKKPPSATRT
          ..SRKKVK.K.P...QDSKKPPSA..T
Retrocopy TYSRKKVKWKHPQGTQDSKKPPSARHT

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	5.91 RPM
SRP017611_kidney	0.00 RPM	7.50 RPM
SRP017611_liver	0.00 RPM	3.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1698 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1698 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010139	1 retrocopy	retro_amel_672,
Callithrix jacchus	ENSCJAG00000012487	1 retrocopy	retro_cjac_538,
Equus caballus	ENSECAG00000011050	1 retrocopy	retro_ecab_126,
Felis catus	ENSFCAG00000004273	1 retrocopy	retro_fcat_757,
Oryctolagus cuniculus	ENSOCUG00000017013	1 retrocopy	retro_ocun_1698 ,
Otolemur garnettii	ENSOGAG00000008255	1 retrocopy	retro_ogar_2914,
Pteropus vampyrus	ENSPVAG00000010097	1 retrocopy	retro_pvam_1022,
Tupaia belangeri	ENSTBEG00000009745	1 retrocopy	retro_tbel_3215,
Tursiops truncatus	ENSTTRG00000004799	1 retrocopy	retro_ttru_1165,