RetrogeneDB ID: retro_cjac_1961

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:133410581..133410983(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033912
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NABP2
• Ensembl ID: ENSCJAG00000011455
• Aliases: None
• Description: nucleic acid binding protein 2 [Source:HGNC Symbol;Acc:28412]

Sequence

>retro_cjac_1961
GTTTTCAAAGGTTGTCTGACACTGTATACTGGCTGCAAGGATAATCTGCAGAAGACTGGAGAATTCTGTATGATTTATAC
TGAGGTTCCTGACTTCAGTGAGTCAAACCCAGAGTACAGCACCCAGCAGGCACTCAACAAGGCAGTGCAGAACGACGGCA
ACCCTTCAGCTTCCCTGCCTATCACCAAACCCCCTGCTGCTTCTCCAGCCTCTGAGAACCAGAACAAGAAGGGACTTAGT
GTCCCACCAGGTCCTGGTGATGGCCCACATCCCCCGCTTACTCCCTCCCACCTGCTCAGCACCCGAATCACCTGAAGCCA
GCCCAACCACATACCTGCAGGCCTGTCTGGCCTTTCCAGCAACTCTGTTAGTAATGGCAAAGAAACCCGGAGGAGCAGCA
AG

Alignment

ORF - retro_cjac_1961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.36 %
• Parental protein coverage: 63.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFKGCLTLYTGRGGDLQKIGEFCMVYSEVPNFSEPNPEYSTQQAPNKAVQNDSNPSASQPTTGPPAASPA
          VFKGCLTLYTG....LQK.GEFCM.Y.EVP.FSE.NPEYSTQQA.NKAVQND.NPSAS.P.T.PPAASPA
Retrocopy VFKGCLTLYTGCKDNLQKTGEFCMIYTEVPDFSESNPEYSTQQALNKAVQNDGNPSASLPITKPPAASPA

Parental  SESQNGNGLSAPSGPGGGPHPPHTPSHPPSTRITRSQPNHTPAGPPGPSSNAVSNGKETRRSSK
          SE.QN..GLS.P.GPG.GPHPP.TPSH..STRIT.SQPNH.PAG..G.SSN.VSNGKETRRSSK
Retrocopy SENQNKKGLSVPPGPGDGPHPPLTPSHLLSTRIT*SQPNHIPAGLSGLSSNSVSNGKETRRSSK

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	0.02 RPM	2.97 RPM
SRP051959_heart	0.02 RPM	2.35 RPM
SRP051959_kidney	0.00 RPM	3.71 RPM
SRP051959_liver	0.00 RPM	2.56 RPM
SRP051959_lung	0.00 RPM	2.75 RPM
SRP051959_lymph_node	0.00 RPM	2.12 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.00 RPM
SRP051959_spleen	0.00 RPM	2.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1961 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1961 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002798	1 retrocopy	retro_btau_545,
Callithrix jacchus	ENSCJAG00000011455	1 retrocopy	retro_cjac_1961 ,
Dasypus novemcinctus	ENSDNOG00000013517	1 retrocopy	retro_dnov_1189,
Erinaceus europaeus	ENSEEUG00000001325	1 retrocopy	retro_eeur_1,
Gorilla gorilla	ENSGGOG00000009050	1 retrocopy	retro_ggor_2094,
Macropus eugenii	ENSMEUG00000004485	4 retrocopies	retro_meug_1118, retro_meug_123, retro_meug_1835, retro_meug_540,
Mustela putorius furo	ENSMPUG00000001297	1 retrocopy	retro_mputfur_59,
Sarcophilus harrisii	ENSSHAG00000002240	1 retrocopy	retro_shar_493,