RetrogeneDB ID: retro_ocun_1684

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018762:550877..551704(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027138
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZDHHC2
• Ensembl ID: ENSOCUG00000014585
• Aliases: None
• Description: zinc finger, DHHC-type containing 2 [Source:HGNC Symbol;Acc:18469]

Sequence

>retro_ocun_1684
AGAGAAAGAATTGTTGGAGAACCAAGAGGACAACCCCATCAGGAAGTTCTTAGGCGAGCAGCCAAGGATCTTCCCATTTT
TACCAGGACCATGACTGGAGCCATCCGCTACTGTGACAGATGCCAACTTATAAAACCAGATCACTGCCATCATTGTTCCA
TCTGCAATAAATGTATTTTGAAGATGGATCATCATTGCCCATGGGTGAACAATTGTGTGGGAATTTCAGATTATAAATTC
TTCCTCCTTTTCCTGGCTTATTATCTGCTGTACTGCCTTTTTATCACTGCTACAGACTTACAGTATATTGTCAAATTTTG
GACAAGTGGTCTACCAGAGACTCAAGCCAAGTTCCATATGCTGTTTCTATTCTTTGCTGCAGCTAGTTTTCTGTCAGTTT
ATCTTCTCTATTTGGCTATCATTGTTGGCTAGTCGGCAAAAATAAATCTACATTAGAGGCATTCAGGAGTCCAGTATCTT
GACATGGAACCAATAAGAATGGATTCAGCTTAGGTCTCAGTAAAAATAATGAGACAAGTTTTTGGTGATGAGAAGAAGTA
CTGGTTGTTACCCATTTTTTCACATCTGTCTGATGGCTGTTCCTTCCCAACTTGCCTTGTTAACCAGGATCCTGAACAAC
CATCTACTCCTGCAGGACTGAATTCAACAGCTAAAAATCCTGAAAACCATCAGTTCCTGCAAATCCATAGAGAGAATTCC
AGAGCCACCTTCTCACTGACTCGCAGTCTTGGACAGAAAGCAACATAAGCCCTGGAAGAGGCAAAGATCCTATGAGCAAT
CCTGTATTAACCATGGAGAATGAGACT

Alignment

ORF - retro_ocun_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.3 %
• Parental protein coverage: 83.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KELLEREPRGEAHQEVLRRAARDLPIYTRTMSGAIRYCDRCQLIKPDRCHHCSVCDKCILKMDHHCPWVN
          .E....EPRG..HQEVLRRAA.DLPI.TRTM.GAIRYCDRCQLIKPD.CHHCS.C.KCILKMDHHCPWVN
Retrocopy RERIVGEPRGQPHQEVLRRAAKDLPIFTRTMTGAIRYCDRCQLIKPDHCHHCSICNKCILKMDHHCPWVN

Parental  NCVGFSNYKFFLLFLAYSLLYCLFIAATDLQYFVKFWTNGLPDTQAKFHIMFLFFAAAM-FSVSLSSLFG
          NCVG.S.YKFFLLFLAY.LLYCLFI.ATDLQY.VKFWT.GLP.TQAKFH..FLFFAAA..FSVSLSSLFG
Retrocopy NCVGISDYKFFLLFLAYYLLYCLFITATDLQYIVKFWTSGLPETQAKFHMLFLFFAAAS<FSVSLSSLFG

Parental  YHCWLVSKNKSTLEAFRSPVFRHGTDKNGFSLGFSKN-MRQVFGDEKKYWLLPIFSSLGDGCSFPTCLVN
          YHCWLV.KNKSTLEAFRSPV..HGT.KNGFSLG.SKN.MRQVFGDEKKYWLLPIFS.L.DGCSFPTCLVN
Retrocopy YHCWLVGKNKSTLEAFRSPVS*HGTNKNGFSLGLSKN>MRQVFGDEKKYWLLPIFSHLSDGCSFPTCLVN

Parental  QDPEQPSTPAGLNSTTKNPENHQF-PAKPLRESQSHLLTDSQSWTESNINPGRGKAGMSNPALTMENET
          QDPEQPSTPAGLNST.KNPENHQF.PA.P.RE.QSHLLTDSQSWTESNI.PGRGK..MSNP.LTMENET
Retrocopy QDPEQPSTPAGLNSTAKNPENHQF<PANP*REFQSHLLTDSQSWTESNISPGRGKDPMSNPVLTMENET

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	0.28 RPM	29.69 RPM
SRP017611_kidney	0.00 RPM	8.01 RPM
SRP017611_liver	0.00 RPM	1.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1684 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011824	1 retrocopy	retro_cjac_934,
Oryctolagus cuniculus	ENSOCUG00000014585	2 retrocopies	retro_ocun_1684 , retro_ocun_1725,