RetrogeneDB ID: retro_ocun_761

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:90440184..90440770(-)
• Located in intron of: ENSOCUG00000003108

Retrocopy information

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

Parental gene information

• Parental gene symbol: HUS1
• Ensembl ID: ENSOCUG00000027263
• Aliases: None
• Description: HUS1 checkpoint homolog (S. pombe) [Source:HGNC Symbol;Acc:5309]

Sequence

>retro_ocun_761
ATGAGATTGTCGTTGGAGAACTTCTCTCTAACCTTGAAGACTGCCCAGAGTGTCAGGGCCTTGAACATGAAGCTGACCAG
TCAGCACTCCCCATGCCTCACCATCTCCTCCGTGGAGCTGATTTCTGTGTCAAGCAGTGGTCGCATTGTGACACATGGCA
TCCCGACAAAAGTTATTCCTAGAAGATTCTAGAAGAACCTCCAGGAGCCCTCTGTCCCAGATCCTGACGTTAGCTTTTAT
TTACCTGTCCTGAAGACCACGAGGAGTGTTGTGGACAAGACGACAAACAGCAGCAGCCACCTTGTCACTGGGGCAAACCT
CAACGGAGAACTGAACTTGAACACAGAAACTGAACTAGCGTGCGTGACGGCCCCAGAGAGCTCAGAAACTCCCCCGCCGC
TGGCCTCTGAAGATGCCTCGCAAGACAGAAGCCAGAACAAATGACTGAAGTGCAAATAGATTTCAAGAAGCCCATGAGGC
TCCTTGCCGGACAGCAGGTGAACGCCGCAAAAGCCCTATGCGATACTGTGCATAACAGGATTGTTCATTTCGATTGCTTC
CTGACAGCGTTTCCCTCCAGTATTTC

Alignment

ORF - retro_ocun_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.16 %
• Parental protein coverage: 75.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LELTSENLARALKTAQNARALKVKLTNRHFPCLTV-SVELISVSSSSRIVTHDIPIKVIPRRLWRDFREP
          ..L..EN....LKTAQ..RAL..KLT..H.PCLT..SVELISVSSS.RIVTH.IP.KVIPRR......EP
Retrocopy MRLSLENFSLTLKTAQSVRALNMKLTSQHSPCLTISSVELISVSSSGRIVTHGIPTKVIPRRF*KNLQEP

Parental  CIPDSDVSIYLPVLKTMRSVVEKMKNISNHLVIEANLNGELNLKIETELVCVTTHFRDLGNPPLASENAS
          ..PD.DVS.YLPVLKT.RSVV.K..N.S.HLV..ANLNGELNL..ETEL.CVT........PPLASE.AS
Retrocopy SVPDPDVSFYLPVLKTTRSVVDKTTNSSSHLVTGANLNGELNLNTETELACVTAPESSETPPPLASEDAS

Parental  QDRS-PDQMAEVQIDIRKLLQLLAGQQVNPTRALCNIVHNRIVHFD-LLHEDVSLQYF
          QDRS.P.QM.EVQID..K...LLAGQQVN...ALC..VHNRIVHFD.LL...VSLQYF
Retrocopy QDRS<PEQMTEVQIDFKKPMRLLAGQQVNAAKALCDTVHNRIVHFD<LLPDSVSLQYF

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	0.11 RPM	7.01 RPM
SRP017611_kidney	0.71 RPM	5.98 RPM
SRP017611_liver	0.23 RPM	2.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_761 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_761 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001764	4 retrocopies	retro_chof_1438, retro_chof_1958, retro_chof_2084, retro_chof_898,
Dipodomys ordii	ENSDORG00000006582	1 retrocopy	retro_dord_182,
Echinops telfairi	ENSETEG00000009941	2 retrocopies	retro_etel_1764, retro_etel_1797,
Nomascus leucogenys	ENSNLEG00000004497	1 retrocopy	retro_nleu_2321,
Oryctolagus cuniculus	ENSOCUG00000027263	1 retrocopy	retro_ocun_761 ,
Otolemur garnettii	ENSOGAG00000012683	1 retrocopy	retro_ogar_1,
Pongo abelii	ENSPPYG00000025821	1 retrocopy	retro_pabe_151,
Sorex araneus	ENSSARG00000012348	1 retrocopy	retro_sara_391,
Ictidomys tridecemlineatus	ENSSTOG00000027204	1 retrocopy	retro_itri_151,