RetrogeneDB ID: retro_ocun_1527

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:112705375..112705720(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSOCUG00000001882
• Aliases: None
• Description: family with sequence similarity 206, member A [Source:HGNC Symbol;Acc:1364]

Sequence

>retro_ocun_1527
AGCATTTCCTATCAGATCAATGCCAACTGTAGCAGACTCCAGAATAGGGTCTCTGGGGACTTTAAGAGGGTGCACAGTTT
CTAACAGAATTTGCACCTCAGGGTAAGATTTCCTGCTCAGGTGGAGGAGAACGTACCGTATCCAGCTGTGTGAGAGGACG
GTTGATGGAAGTGGATGAAATCATCCTCCATGAGCCATCTGTTCTTTAAGAAAGCCATCGCTGAAGGTTACACTGCAGTT
GTGTTACCCAAATTTGAAGAAAGTAAAAGCGAAACAGAAGGCTTCCTGACACAAAAGCCATGTGAAGAAGTTGTGAAATG
CATTAATGCCACAGCAGCTACATCC

Alignment

ORF - retro_ocun_1527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.83 %
• Parental protein coverage: 59.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SISYQISTNCSRLQNKVSGKFKR-GAQFLTEFAPLCKIYCSDGEEYTISSCVRGRLMEVNENILHEPSIL
          SISYQI..NCSRLQN.VSG.FKR.GAQFLTEFAP..KI.CS.G.E.T.SSCVRGRLMEV.E.ILHEPS.L
Retrocopy SISYQINANCSRLQNRVSGDFKR<GAQFLTEFAPQGKISCSGGGERTVSSCVRGRLMEVDEIILHEPSVL

Parental  QE-KPS-TEGYIAVVLPKFEESKSITEGLLTQKQYEEVVLKRADATTATS
          .E.KPS..EGY.AVVLPKFEESKS.TEG.LTQK..EEVV.K...AT.ATS
Retrocopy *E<KPS<AEGYTAVVLPKFEESKSETEGFLTQKPCEEVV-KCINATAATS

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	7.78 RPM
SRP017611_kidney	0.00 RPM	3.65 RPM
SRP017611_liver	0.00 RPM	1.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1527 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1527 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527 ,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583,