RetrogeneDB ID: retro_cjac_757

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:12026191..12026923(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007036
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008389
• Aliases: None
• Description: None

Sequence

>retro_cjac_757
ATGGCATCTGGGGATTTCTGCTCATTTGGAGAAGGCATAGAAATACTTCAGCGAGAAGTGTGCAGGAAACAACTTCCTCC
TTGTAAACTGAGTAAAGAGGACCTGTTACAGAACCCATACTTCAGCAAGCTTCTACTGAGTCTCTCACAGCACGTGGATG
AGAGCGGCTTAAGCCTCACCCTAGCAAAGGACCAGGCTCAGGCATGGAAGGAAGTTCGACTGCATAAGACAACATGGTTG
AGGTCTGAGATTTTACATAGAGTCATTCAAGAGTTGCTTGTGGATTACTATGTGAAGATGCAAGATACAAATTTAACTTC
TGAGGACAAAAAGTTTCATGAGACCCTTGAACAACGGCTACTTGTAGCTGAACTGACTCGGCTCTTAGGTCCTAGCCAGG
AGAGGGAGATACCTCCACTGCCAGGGCTGGAGGAAGCAGACCTTCTGGAACTCATACCACTCTCCGAGGATTTTGCGTGG
ATGAGGGCTCGACTACAGCAAGAAGTAGAGGAGCAGCTCAAAAAGAAATGTTTCACTCTCCTCTGCTACTATGATCCCAA
CTCAGATGCTGACAGTGAAACTGTGAAGGCAGCAAAGGTGTGGAAACTCGCAGAGGTCCTGGTGGGTGAGCAGCAGCAGT
GCCAGGATGCCAAGAGCCAGCAGAAGGAGCAGATGGTGCTGCTGGAGAAGAAGAATGCCACCTACTCCCAGGTGCTTCTC
CGCTGCCTCACT

Alignment

ORF - retro_cjac_757 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.9 %
• Parental protein coverage: 66.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGDFCSFGEGIEILQ-QVCRKQLPPCNLSKEDLLQNPYFSKLLLSLSQHMDESGLSLTLAKEQAQAWK
          MASGDFCSFGEGIEILQ..VCRKQLPPC.LSKEDLLQNPYFSKLLLSLSQH.DESGLSLTLAK.QAQAWK
Retrocopy MASGDFCSFGEGIEILQREVCRKQLPPCKLSKEDLLQNPYFSKLLLSLSQHVDESGLSLTLAKDQAQAWK

Parental  EVRLHKTTWLRSEILHRVIQELLVDYYVKMQDTNLTSEDKKFHETLEQRLLVTELTRLLGPSQEREIPPL
          EVRLHKTTWLRSEILHRVIQELLVDYYVKMQDTNLTSEDKKFHETLEQRLLV.ELTRLLGPSQEREIPPL
Retrocopy EVRLHKTTWLRSEILHRVIQELLVDYYVKMQDTNLTSEDKKFHETLEQRLLVAELTRLLGPSQEREIPPL

Parental  LGLEKADLLELMPLSEDFVWMRARLQQEVEEQLKKKCFTLLCYYDPNSDADSETVKAAKVWKLAEVLVGE
          .GLE.ADLLEL.PLSEDF.WMRARLQQEVEEQLKKKCFTLLCYYDPNSDADSETVKAAKVWKLAEVLVGE
Retrocopy PGLEEADLLELIPLSEDFAWMRARLQQEVEEQLKKKCFTLLCYYDPNSDADSETVKAAKVWKLAEVLVGE

Parental  QQQCQDAKSQQKEQMVLLEKKNATYSQVLLRCLT
          QQQCQDAKSQQKEQMVLLEKKNATYSQVLLRCLT
Retrocopy QQQCQDAKSQQKEQMVLLEKKNATYSQVLLRCLT

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	0.09 RPM	8.48 RPM
SRP051959_heart	0.12 RPM	12.59 RPM
SRP051959_kidney	0.09 RPM	20.46 RPM
SRP051959_liver	0.06 RPM	11.09 RPM
SRP051959_lung	0.10 RPM	16.43 RPM
SRP051959_lymph_node	0.02 RPM	16.14 RPM
SRP051959_skeletal_muscle	0.02 RPM	5.50 RPM
SRP051959_spleen	0.74 RPM	16.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_757 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_757 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008389	1 retrocopy	retro_cjac_757 ,
Dasypus novemcinctus	ENSDNOG00000002575	1 retrocopy	retro_dnov_712,
Homo sapiens	ENSG00000092036	1 retrocopy	retro_hsap_469,
Gorilla gorilla	ENSGGOG00000007504	1 retrocopy	retro_ggor_447,
Myotis lucifugus	ENSMLUG00000012934	1 retrocopy	retro_mluc_1946,
Otolemur garnettii	ENSOGAG00000000586	1 retrocopy	retro_ogar_382,
Pongo abelii	ENSPPYG00000005651	1 retrocopy	retro_pabe_265,
Pan troglodytes	ENSPTRG00000006153	1 retrocopy	retro_ptro_352,