RetrogeneDB ID: retro_ocun_996

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:50208424..50208837(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSOCUG00000009156
• Aliases: None
• Description: SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Sequence

>retro_ocun_996
GAGATGTTGGGTGTGGGGGACTTTAATTGTGAGCTAAGTGTCCAGATCATCAATGTGTCCCTAACCCTGAAGCACCAAAG
TGGAAGTCTGAGAATTTTGAAGGAAGTACATCAACAGGTGTTAAAAGGAAGGGAAAGTTCACCCAGGGAGTCAGCCAATA
GAACCTAGACAGGGCATTAGAAACACAAGGTATTTGGTACTGGCTTTGCATCATTCCCATGGGTGGCACTTACCTCATTC
AGTCTGCTCCAGCTTTCAATGCGGATTACATTGTGGGGCTGCAGCTGGCAGAAAAAAAGCGGCTGTAAGATTGTCAGTGA
AATAAAAGCCAGTGTTAGATGGCAGACAGAACACATGTAGCAATTACTGGAACACCTGCTGAAGGAAGGGTGCCCTGGCT
GGACTTGTATGCC

Alignment

ORF - retro_ocun_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.84 %
• Parental protein coverage: 54.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGR-GKFAQDVSQDDLIRAIKKLKALGTG
          .MLGVGDF..EL.VQII.V.L.LKH..G.L..L.E.HQQVLKGR.GKF.Q.VSQ..L.RA..........
Retrocopy EMLGVGDFNCELSVQIINVSLTLKHQSGSLRILKEVHQQVLKGR<GKFTQGVSQ*NLDRAL-ETQGIWYW

Parental  FGIIPVGGTYLIQSVPAELNMDHTVVLQLAE-KNGYVTVSEIKASLKWETERARQVLEHLLKEG-LAWLD
          ..IIP.GGTYLIQS.PA..N.D..V.LQLAE.K.G...VSEIKAS..W.TE...Q.LEHLLKEG...WLD
Retrocopy LCIIPMGGTYLIQSAPA-FNADYIVGLQLAE>KSGCKIVSEIKASVRWQTEHM*QLLEHLLKEG<VPWLD

Parental  LQA
          L.A
Retrocopy LYA

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	28.97 RPM
SRP017611_kidney	0.00 RPM	51.79 RPM
SRP017611_liver	0.00 RPM	20.42 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_996 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_996 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996 ,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,