RetrogeneDB ID: retro_cjac_742

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:122937913..122938275(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006704
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNAPIN
• Ensembl ID: ENSCJAG00000010373
• Aliases: None
• Description: SNAP-associated protein [Source:HGNC Symbol;Acc:17145]

Sequence

>retro_cjac_742
GCAGGGGCTGGTTCCGCTGCTGTGTCGGGGGCAGGGACCCCTGTGGCGGGGCCCACAGGCCGCGACCTCTTCGCTGAAGG
GCTGCTGGAGTTCCTGCGACCTGCTGTGCAGCAGCTCGACTCTCACGTGCACACCGTCAGAGAGAGCCAGGTGGAGCTCC
GGGAGCAAATTGATAACCTAGCCACAGAACTGTGCCGCATCAATGAGGATCAGAAGGTGGCCCTGGATCTTGACCCCTAT
GTTAAGAAGCTACTTAATGCTCAGCGACGCGTTGTCTTGGTCAACAACATTCTACAGAATGCTCAGGACGGCTGAGGTGG
CTAAACCACAGTGTTGCCAAGGAAACAGCCCGCAGGAGAGCA

Alignment

ORF - retro_cjac_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.9 %
• Parental protein coverage: 88.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGAGSAAVSGAGTPVAGPTGRDLFAEGLLEFLRPAVQQLDSHVHAVRESQVELREQIDNLATELCRINED
          AGAGSAAVSGAGTPVAGPTGRDLFAEGLLEFLRPAVQQLDSHVH.VRESQVELREQIDNLATELCRINED
Retrocopy AGAGSAAVSGAGTPVAGPTGRDLFAEGLLEFLRPAVQQLDSHVHTVRESQVELREQIDNLATELCRINED

Parental  QKVALDLDPYVKKLLNARRRVVLVNNILQNAQE-RLRRLNHSVAKETARRRA
          QKVALDLDPYVKKLLNA.RRVVLVNNILQNAQ..RLR.LNHSVAKETARRRA
Retrocopy QKVALDLDPYVKKLLNAQRRVVLVNNILQNAQD<RLRWLNHSVAKETARRRA

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	2.95 RPM
SRP051959_heart	0.00 RPM	5.75 RPM
SRP051959_kidney	0.00 RPM	6.72 RPM
SRP051959_liver	0.00 RPM	4.38 RPM
SRP051959_lung	0.00 RPM	6.80 RPM
SRP051959_lymph_node	0.00 RPM	6.48 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.22 RPM
SRP051959_spleen	0.00 RPM	7.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_742 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_742 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003301	1 retrocopy	retro_chof_723,
Callithrix jacchus	ENSCJAG00000010373	1 retrocopy	retro_cjac_742 ,
Dasypus novemcinctus	ENSDNOG00000015216	1 retrocopy	retro_dnov_1023,
Mus musculus	ENSMUSG00000001018	1 retrocopy	retro_mmus_1257,
Sorex araneus	ENSSARG00000013451	1 retrocopy	retro_sara_19,