RetrogeneDB ID: retro_ocun_1053

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:82923975..82924477(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000013440
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAK16
• Ensembl ID: ENSOCUG00000008735
• Aliases: None
• Description: MAK16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:13703]

Sequence

>retro_ocun_1053
GTGGGGCTCAGTAAGAACTACAAGAAAGCACTGGGGCAAATAAGGCAAGAATCTCGTTTAGTGGTCCCTTTCATCTGACG
TAAGTGTAAGCAGAGATTCACCAAGATAACCCAGTGCCTAAGTCAAGTTAGAAAACTTACACTAAGACGACAAAGGGAAC
TTGCTTCTTTGAGTAGGAAGGTGGGTGTAGGGAGAAAAGAGGAGAGAAAAAGGCATCAGTCGCTGCCTGGTTGGACAATG
CCATTGAAAAGGAATACTGGAAAGACTGCAACAAGATACGTATGGCAGCATCTCCAACCTCCCCATTCATGCCTTCCACA
AGGCCCTGGAGCAACAGGAGGCGGAGAGGGAAAAGATGACGAAGATGCGGGGGAAAAGAGAATTTGTGGAGGATAAGGGG
ATGGATGAGAGTGATATGAGTCATTTTGAGGATATGGGGCAACTGGATGCCAGCAGTGATGAAGACTGGGATGATAGATC
CTCCAGTGAAGAGGAAGACAAG

Alignment

ORF - retro_ocun_1053 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.53 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRLSKNYEKALEQIDENLIYWPRFIRHKCKQRFTKITQYLIRIRKLTLKRQRKLVPLSKKV-ERREKRRE
          V.LSKNY.KAL.QI.........FI..KCKQRFTKITQ.L...RKLTL.RQR.L..LS.KV...REKR.E
Retrocopy VGLSKNYKKALGQIRQESRLVVPFI*RKCKQRFTKITQCLSQVRKLTLRRQRELASLSRKV<GCREKRGE

Parental  EKALIAAQLDNAIEKE-LLERLKQDTYGDIYNFPIHAFDKALEQQEAESDSSDEEKDD-EDDDDDDVGKR
          .KA..AA.LDNAIEKE..LERL.QDTYG.I.N.PIHAF.KALEQQEAE...........E...D......
Retrocopy KKASVAAWLDNAIEKE<ILERLQQDTYGSISNLPIHAFHKALEQQEAEREKMTKMRGKREFVEDKGMDES

Parental  EFVEDEEVDESDISDFEDMDKLDASSDEDQ
          .....E.....D.S..ED.D....S..ED.
Retrocopy DMSHFEDMGQLDASSDEDWDDRSSSEEEDK

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	14.02 RPM
SRP017611_kidney	0.00 RPM	11.86 RPM
SRP017611_liver	0.00 RPM	5.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1053 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1053 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1053 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009081	5 retrocopies	retro_chof_2336, retro_chof_2538, retro_chof_531, retro_chof_867, retro_chof_948,
Dasypus novemcinctus	ENSDNOG00000008424	1 retrocopy	retro_dnov_624,
Latimeria chalumnae	ENSLACG00000018758	1 retrocopy	retro_lcha_67,
Macropus eugenii	ENSMEUG00000006945	1 retrocopy	retro_meug_1291,
Myotis lucifugus	ENSMLUG00000002758	1 retrocopy	retro_mluc_590,
Oryctolagus cuniculus	ENSOCUG00000008735	3 retrocopies	retro_ocun_1053 , retro_ocun_1298, retro_ocun_908,
Sus scrofa	ENSSSCG00000015832	1 retrocopy	retro_sscr_917,