RetrogeneDB ID: retro_ocun_1298

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:36499337..36500059(+)
• Located in intron of: None

Retrocopy information

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

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_1298
AAGAAGAGAAAGTGCTACTTGTATATGAAGGTGATAGAATGAGCAGCTTTTCCCAGGAGTATGTGGGAACTGGTTTGGCT
CAGTAAGAACTAGGAGAAACCACTGGAGCAAACAGATGAAAATCTAATCTACTGGCCCCATTTCTTTTGAAACAAATGTA
AGCAGAGATTCACCAAGACAACCCAGTACCTAATTTGAATTAGAAAACATACATTAAAATGACAGAGGAAACTTGCTCCT
CTGAGTAACAAGGTTGATCATAGGAAGAAAAGAAGAGAGGAAAAGTCATTAATAGCTGCTCAGTTGGACAATGCCACTGA
AAAGGAATTACTGGAAAGACTGAAACAAGATAGGTGTGGTGACATCCACAGCTTTCTCATTCATGACTTCAACAAGGCCC
TGGAACAACAGGGGGCAGAGAGGGACTCTTCAGATGAGGAAAAAGATGATGAAGATGATGATGAAGGTGTGCAACAAAGA
GAATCTGTGGAAGATGAGGAGTGAGATGAAAGTGATTTAAGTGATTTTGAGGATATGGATTAATTGGATGCCAGCAGTGA
TGGAGACCAGGATGGGAAATCCTCTGGAGAAGAGGAAGAAAAGTCCTTAATGCAAAACACAAAGACAAAGCACCCTGGAA
AGGACTTTTTGGGAGAAAAGTAACCTATGTAGAGATAGAGTATGAGCAGGAAACAGAGCCTCTGGCCAAGGCCAAAACCA
CT

Alignment

ORF - retro_ocun_1298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.95 %
• Parental protein coverage: 81.21 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKGQCYLYMKVIERAAFPRRMWERVRLSKNYEKALEQIDENLIYWPRFIRHKCKQRFTKITQYLIRIRKL
          .K..CYLYMKVIE.AAFPR.MWE.V.LSKN.EK.LEQ.DENLIYWP.F...KCKQRFTK.TQYLI.IRK.
Retrocopy KKRKCYLYMKVIE*AAFPRSMWELVWLSKN*EKPLEQTDENLIYWPHFF*NKCKQRFTKTTQYLI*IRKH

Parental  TLKRQRKLVPLSKKVERREKRREEKALIAAQLDNAIEKELLERLKQDTYGDIYNFPIHAFDKALEQQEAE
          TLK.QRKL.PLS.KV..R.KRREEK.LIAAQLDNA.EKELLERLKQD..GDI..F.IH.F.KALEQQ.AE
Retrocopy TLK*QRKLAPLSNKVDHRKKRREEKSLIAAQLDNATEKELLERLKQDRCGDIHSFLIHDFNKALEQQGAE

Parental  SDSSDEEKDDEDDDDDDVGKREFVEDEEVDESDISDFEDMDKLDASSDEDQDGKSSSEEEEKS-FNAKHK
          .DSSDEEKDDEDDD...V..RE.VEDEE.DESD.SDFEDMD.LDASSD.DQDGKSS.EEEEKS..NAKHK
Retrocopy RDSSDEEKDDEDDD-EGVQQRESVEDEE*DESDLSDFEDMD*LDASSDGDQDGKSSGEEEEKS<LNAKHK

Parental  GKTPLKGPLRRKRAYVEIEYEQETEPTAKAKTT
          .K.P.KG...RK..YVEIEYEQETEP.AKAKTT
Retrocopy DKAPWKGLFGRKVTYVEIEYEQETEPLAKAKTT

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_1298 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1298 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1298 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,