RetrogeneDB ID: retro_cjac_3968

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286450.1:451456..451925(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HHEX
• Ensembl ID: ENSCJAG00000008627
• Aliases: None
• Description: hematopoietically expressed homeobox [Source:HGNC Symbol;Acc:4901]

Sequence

>retro_cjac_3968
CATGCCCTGCTCTGCCATGACCCCCTGCAGAAACCTCTACTTTGGAGCTCCTTCTTGCAGAAGTCTCTGCATAAAAGGAA
AGGAGGCCAGGTGAGGTTCTCCAACGACCAGACCATCAAGCTGGAGAAGTTCGAGATGCAGAAATACCTCTCTCTGCCCG
AGAGAAAGCATCTGGCCAAGATGCTGCAGCTTAGCAAGAGACAGGTCAAAACCTGGTTTAAGAATCGACATGCTAAATGG
AGGAGACTAAAACAGGAGAACCCTCAAAGCAATAAAAAATGAAGAACTGGAAAGTTTGGACAATTCCTGTGACCAGAGGC
AAGATTTGCCCAGTGAACAGAATAAATGTGCTTCTTTAGATAGCTCTCAGTGTTCGCCCTCCCCTGCCTCTTAGGAAGAC
CTTGATTCAGAGATTTCAGAGGATTCGGATCAGGAAGTGGACATTGAGGGTGATAAAGGATATTTTAAT

Alignment

ORF - retro_cjac_3968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.24 %
• Parental protein coverage: 58.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HALLRHDPLGKPLLWSPFLQRPLHKRKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQV
          HALL.HDPL.KPLLWS.FLQ..LHKRKGGQVRFSNDQTI.LEK.FE.QKYLS.PERK.LAKMLQLS.RQV
Retrocopy HALLCHDPLQKPLLWSSFLQKSLHKRKGGQVRFSNDQTIKLEK-FEMQKYLSLPERKHLAKMLQLSKRQV

Parental  KTWFQNRRAKWRRLKQENPQSNKK-EELESLDNSCDQRQDLPSEQNKGASLDSSQCSPSPASQEDLESEI
          KTWF.NR.AKWRRLKQENPQSNKK.EELESLDNSCDQRQDLPSEQNK.ASLDSSQCSPSPAS.EDL.SEI
Retrocopy KTWFKNRHAKWRRLKQENPQSNKK>EELESLDNSCDQRQDLPSEQNKCASLDSSQCSPSPAS*EDLDSEI

Parental  SEDSDQEVDIEGDKGYFN
          SEDSDQEVDIEGDKGYFN
Retrocopy SEDSDQEVDIEGDKGYFN

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	1.13 RPM
SRP051959_heart	0.00 RPM	3.03 RPM
SRP051959_kidney	0.00 RPM	1.46 RPM
SRP051959_liver	0.00 RPM	21.47 RPM
SRP051959_lung	0.00 RPM	7.56 RPM
SRP051959_lymph_node	0.00 RPM	5.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.57 RPM
SRP051959_spleen	0.00 RPM	9.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3968 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3968 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008627	1 retrocopy	retro_cjac_3968 ,
Sus scrofa	ENSSSCG00000010472	1 retrocopy	retro_sscr_1005,