RetrogeneDB ID: retro_cjac_934

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:92127153..92127708(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC2
• Ensembl ID: ENSCJAG00000011824
• Aliases: None
• Description: None

Sequence

>retro_cjac_934
ATTTGGTCATACTGGAAAACTATCTTTACATTACCAATGATTTCTTCAAAAGAATTCCATCTCTCTTATGCAGAGAAAGG
ATTGTCAGAGACAGAGCCAAGAGGAGAAGCCCATCAGGAAGTTCTTAGGTGAGTAGCCCAGGATCTTTCCATCTACACCA
AGACCACGTCAGGAGTAATCCGATATTGTGACAGATGCCAACTTATAAAACCAGTTCGCTGCCATCACTGTTCTGCCCGT
GATAAATGTATTTTGAAGATGGATCATCATTGCCCATGGGTAAACAATTGTCTTAGATTTTCAAATTAAAGTTCTTCGGC
CTTTTCTTGGCTTATTCTCTGCTCTACTGCCTTTTATTTTGCGGCAACAGATTTACAGTGTATTTTATCAAATTTTGGAC
AAATGGCCTACCTGTTACTCAAGCCAAGTTCCATAATTACATTTTTATTCTTTGCTGCAGCTACGTTTTCTGTCAGCTTG
TCTTCTCTGTTTCGCTATCATTGTTGGCTAGTCAGCAAAACTAAATCTACATTAGAGGCATTCAGAAGTCCAGTA

Alignment

ORF - retro_cjac_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.21 %
• Parental protein coverage: 50.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VWSYWKTIFTLPMNPSKEFHLSYSEKELLEREPRGEAHQEVLRRAAKDLPIYTRTMSGAIRYCDRCQLIK
          .WSYWKTIFTLPM..SKEFHLSY.EK.L.E.EPRGEAHQEVLR..A.DL.IYT.T.SG.IRYCDRCQLIK
Retrocopy IWSYWKTIFTLPMISSKEFHLSYAEKGLSETEPRGEAHQEVLR*VAQDLSIYTKTTSGVIRYCDRCQLIK

Parental  PDRCHHCSVCDKCILKMDHHCPWVNNCVGFSN-YKFFLLFLAYSLLYCLFIAATDLQ-YFIKFWTNGLPD
          P.RCHHCS..DKCILKMDHHCPWVNNC..FSN..KFF.LFLAYSLLYCL.........YFIKFWTNGLP.
Retrocopy PVRCHHCSARDKCILKMDHHCPWVNNCLRFSN<LKFFGLFLAYSLLYCLLFCGNRFTVYFIKFWTNGLPV

Parental  TQAKFH-IMFLFFAAAMFSVSLSSLFGYHCWLVSKNKSTLEAFRSPV
          TQAKFH.I.FLFFAAA.FSVSLSSLF.YHCWLVSK.KSTLEAFRSPV
Retrocopy TQAKFH>ITFLFFAAATFSVSLSSLFRYHCWLVSKTKSTLEAFRSPV

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
SRP051959_colon	0.00 RPM	14.60 RPM
SRP051959_heart	0.00 RPM	6.84 RPM
SRP051959_kidney	0.00 RPM	22.45 RPM
SRP051959_liver	0.00 RPM	21.86 RPM
SRP051959_lung	0.00 RPM	10.13 RPM
SRP051959_lymph_node	0.00 RPM	1.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.06 RPM
SRP051959_spleen	0.00 RPM	11.22 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_934 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_934 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004119	1 retrocopy	retro_cjac_1437,
Callithrix jacchus	ENSCJAG00000011824	1 retrocopy	retro_cjac_934 ,
Oryctolagus cuniculus	ENSOCUG00000014585	2 retrocopies	retro_ocun_1684, retro_ocun_1725,