RetrogeneDB ID: retro_cjac_3991

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286657.1:1561..1968(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031793
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ITGB3BP
• Ensembl ID: ENSCJAG00000016555
• Aliases: None
• Description: integrin beta 3 binding protein (beta3-endonexin) [Source:HGNC Symbol;Acc:6157]

Sequence

>retro_cjac_3991
AATCTGTTTGCTTCTCCCACAAGCTCGAAAGAACAAGAGTACAGAAATGGACTATCAAATGAAAAGGGAAAAAAATGGAA
TCACTCCAGTTTAACTGAAAGCAAAGAATCTACAACAAAAGACAGAGATGAATTCATGATGTTGCTGTCTAAAGTTGAGA
AATTATCAGAAGAAATTATGGAGATAATGCAAAATGTAAGTAGTATGCAGGCTTTGGAGGGCAGGAGAGAGCTTGAAAAT
CTCACTGGAATCTCCTGTGGATCACATTTCTTAAAAAGAGAAATGCATAAAACCAAAGAACTAATGACAAAAGTAACTAA
AGAAAAACTGTTTCAAAAGAGTTAGGACTTCCTCACAGAGGATCGTGTCATCGTGACAGCTGTAAATTCCTTAAAGCCAT
TTTAAAC

Alignment

ORF - retro_cjac_3991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 76.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLFASPTSSKEQEYGNGLSNEKRKKLNHPSLTESKESTTKDNDEFMMLLSKVEKLSEEIVEIMQNLSSIQ
          .LFASPTSSKEQEY.NGLSNEK.KK.NH.SLTESKESTTKD.DEFMMLLSKVEKLSEEI.EIMQN.SS.Q
Retrocopy NLFASPTSSKEQEYRNGLSNEKGKKWNHSSLTESKESTTKDRDEFMMLLSKVEKLSEEIMEIMQNVSSMQ

Parental  ALEGSRELENLIGISCGSRFLKREMKKTKELMTKVTKRKLFEKS-SVLPHRESCHLDSYEFLKAILN
          ALEG.RELENL.GISCGS.FLKREM.KTKELMTKVTK.KLF.KS...LPHR.SCH.DS..FLKAILN
Retrocopy ALEGRRELENLTGISCGSHFLKREMHKTKELMTKVTKEKLFQKS<LGLPHRGSCHRDSCKFLKAILN

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	2.51 RPM
SRP051959_heart	0.00 RPM	1.09 RPM
SRP051959_kidney	0.00 RPM	1.62 RPM
SRP051959_liver	0.00 RPM	1.15 RPM
SRP051959_lung	0.00 RPM	1.72 RPM
SRP051959_lymph_node	0.00 RPM	2.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.96 RPM
SRP051959_spleen	0.00 RPM	2.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3991 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3991 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3991 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030710	1 retrocopy	retro_btau_747,
Callithrix jacchus	ENSCJAG00000016555	3 retrocopies	retro_cjac_2618, retro_cjac_3850, retro_cjac_3991 ,
Mus musculus	ENSMUSG00000028549	1 retrocopy	retro_mmus_1547,
Rattus norvegicus	ENSRNOG00000009116	1 retrocopy	retro_rnor_1472,
Tursiops truncatus	ENSTTRG00000007480	1 retrocopy	retro_ttru_996,