RetrogeneDB ID: retro_ocun_395

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:139445209..139445719(-)
• Located in intron of: ENSOCUG00000007181

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC4
• Ensembl ID: ENSOCUG00000006160
• Aliases: None
• Description: ER membrane protein complex subunit 4 [Source:HGNC Symbol;Acc:28032]

Sequence

>retro_ocun_395
ATGACAGCCCAAGGGAGCCTGGTCATGAACTGAGGGTAGAACTTCAAATGGGCCACTGAGCTAAGTAGGCCTGGAGGAAA
CAACAGGGACTGAAGTAACCAGGGCAGTGGCCCAGGGAGACTCACTGCATCCAGTCGGTTACTTGGACAAGCAAGTGCCT
GAGTACTATGCAAGAGACAGATGAGACCTTGGTATAGAAGCACTGCTGGGTCATTGCCTCAGGTCCCCTGAAACAGATTC
CTATGAACCTCTTCATCATTTATACATGGCAGGCAATACTATCTCCATCTTTCCTTTATGATGGTGTGTATGATTGCCTG
GTGACCCATTCAAGCACTTATGGCCATTTCAGCCACTTTAAAGATTCTAGGAATTTAAGCCCAGAAAACTTTTCAAGGTT
TTGTGTATCTTAATGGGAACTTGATGGGTTTGGAATTAGCTGGTGACAGGTGCCAGTCTATGGGATTACTGCGTACACAT
GTATCAGAGTTGTTAGCCTTCATTGACCCC

Alignment

ORF - retro_ocun_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.88 %
• Parental protein coverage: 92.9 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTAQGSLVANRGRRFKWAIELSGPGGGSRGRSDRSSG-QGDSLYPVGYLDKQVPDTSVQETDRILVEKRC
          MTAQGSLV.N.G..FKWA.ELS.PGG..R..S...SG.QGDSL.PVGYLDKQVP............E...
Retrocopy MTAQGSLVMN*G*NFKWATELSRPGGNNRD*SNQGSG>QGDSLHPVGYLDKQVPEYYARDR*DLGIEALL

Parental  WDIALGPLKQIPMNLFIMYMAGNTISIFPT-MMVCMMAWRPIQALMAISATFKMLESSSQKFLQGLVYLI
          ......P.......L...YMAGNTISIFP..MMVCM.AW.PIQALMAISAT.K.L....QK..QG.VYL.
Retrocopy GHCLRSPETDSYEPLHHLYMAGNTISIFPL<MMVCMIAW*PIQALMAISATLKILGI*AQKTFQGFVYLN

Parental  GNLMGLALAVYKCQSMGLLPTHASDWLAFIEP
          GNLMGL.LA...CQSMGLL.TH.S..LAFI.P
Retrocopy GNLMGLELAGDRCQSMGLLRTHVSELLAFIDP

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	110.76 RPM
SRP017611_kidney	0.00 RPM	66.29 RPM
SRP017611_liver	0.00 RPM	14.72 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_395 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_395 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005576	2 retrocopies	retro_chof_1859, retro_chof_254,
Dipodomys ordii	ENSDORG00000008407	2 retrocopies	retro_dord_387, retro_dord_581,
Echinops telfairi	ENSETEG00000001688	1 retrocopy	retro_etel_1631,
Felis catus	ENSFCAG00000001736	1 retrocopy	retro_fcat_759,
Macropus eugenii	ENSMEUG00000004615	1 retrocopy	retro_meug_1129,
Microcebus murinus	ENSMICG00000003864	2 retrocopies	retro_mmur_1313, retro_mmur_180,
Oryctolagus cuniculus	ENSOCUG00000006160	4 retrocopies	retro_ocun_1686, retro_ocun_395 , retro_ocun_719, retro_ocun_817,
Ochotona princeps	ENSOPRG00000009190	1 retrocopy	retro_opri_605,
Pteropus vampyrus	ENSPVAG00000003824	1 retrocopy	retro_pvam_386,
Rattus norvegicus	ENSRNOG00000005719	1 retrocopy	retro_rnor_897,
Ictidomys tridecemlineatus	ENSSTOG00000000516	1 retrocopy	retro_itri_1008,