RetrogeneDB ID: retro_ocun_1725

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018825:733075..733950(+)
• Located in intron of: None

Retrocopy information

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

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_1725
TATATATTACCAATGGATCCTTCCAAAGAATTCCATCTCTCTTATGCAGAGAAAGAATTGTTGGAGAGAGACCCAAGAGG
ACAACCCCATCAGAAGGTTCTTAGGCGAGCAGCCAGGGATCTTCCCATTTATACCAGGACCATGACTGGAGCCATCCGCT
ACTGTGACAGATGCCAACTTATAAAACCAGATCACTGCCATCACTGTTCCGTCTGCGATAAATGTATTTTGAAGATGGAT
CATCATTGCCCATGGGTGAACAATTGTGTGGGAATTTCAGATTATAAATTCTTCCTCCTTTTCATGGCTTATTATCTGCT
GTACTGCCTTTTTATCACTGCTACAGACTTACAGTATGTTGTCAAATTTTGGACAAGTGGTCTACCAGATACTCAAGCCA
AGTTCCATATGCTGTTTCTATTCTTTGCTGCAGCTAGTTTTCTGTCAGCTTATCTTCTCTATTTGGCTATCATTGTTGGC
TAGTCAGCAAAAATAAATCTACATTAGAGGCATTCAGGAGTCCAGTATCTCGACATGGAACCAATAAGAATGGATTCAGC
TTAGGTCTCAGTAAAAATAATGAGACAAGTTTTTGGTGATGAGAAGTACTGGTTGTTACCCATTTTTTCACATCTGTCTG
ATGGCTGCTCCTTCCCAACTTGCCTTGTTAACCAGGATCCTGAACAACCATCTACTCCTGCAGGACTGAATTCAACAGCT
AAAAATCCTGAAAACCATCAGTTCCTGCAAATCCATTGAGAGAATTCCAGAGCCACCTTCTCACTGACTCTCAGTCTTGG
ACAGAAAGCAACGTAAGCCCTGGAAGAGGCAAAGCTGCTATGAGCAATCCTGCATTAACCATGGAGAATGAGACT

Alignment

ORF - retro_ocun_1725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 88.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FTLPMNPSKEFHLSYAEKELLEREPRGEAHQEVLRRAARDLPIYTRTMSGAIRYCDRCQLIKPDRCHHCS
          ..LPM.PSKEFHLSYAEKELLER.PRG..HQ.VLRRAARDLPIYTRTM.GAIRYCDRCQLIKPD.CHHCS
Retrocopy YILPMDPSKEFHLSYAEKELLERDPRGQPHQKVLRRAARDLPIYTRTMTGAIRYCDRCQLIKPDHCHHCS

Parental  VCDKCILKMDHHCPWVNNCVGFSNYKFFLLFLAYSLLYCLFIAATDLQYFVKFWTNGLPDTQAKFHIMFL
          VCDKCILKMDHHCPWVNNCVG.S.YKFFLLF.AY.LLYCLFI.ATDLQY.VKFWT.GLPDTQAKFH..FL
Retrocopy VCDKCILKMDHHCPWVNNCVGISDYKFFLLFMAYYLLYCLFITATDLQYVVKFWTSGLPDTQAKFHMLFL

Parental  FFAAAM-FSVSLSSLFGYHCWLVSKNKSTLEAFRSPVFRHGTDKNGFSLGFSKN-MRQVFGDEKKYWLLP
          FFAAA..FSVSLSSLFGYHCWLVSKNKSTLEAFRSPV.RHGT.KNGFSLG.SKN.MRQVFGDE.KYWLLP
Retrocopy FFAAAS<FSVSLSSLFGYHCWLVSKNKSTLEAFRSPVSRHGTNKNGFSLGLSKN>MRQVFGDE-KYWLLP

Parental  IFSSLGDGCSFPTCLVNQDPEQPSTPAGLNSTTKNPENHQF-PAKPLRESQSHLLTDSQSWTESNINPGR
          IFS.L.DGCSFPTCLVNQDPEQPSTPAGLNST.KNPENHQF.PA.PLRE.QSHLLTDSQSWTESN..PGR
Retrocopy IFSHLSDGCSFPTCLVNQDPEQPSTPAGLNSTAKNPENHQF<PANPLREFQSHLLTDSQSWTESNVSPGR

Parental  GKAGMSNPALTMENET
          GKA.MSNPALTMENET
Retrocopy GKAAMSNPALTMENET

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	0.33 RPM	29.69 RPM
SRP017611_kidney	0.00 RPM	8.01 RPM
SRP017611_liver	0.08 RPM	1.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1725 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1725 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 ,