RetrogeneDB ID: retro_cjac_2630

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:85262339..85263007(-)
• Located in intron of: ENSCJAG00000001292

Retrocopy information

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

Parental gene information

• Parental gene symbol: GEMIN2
• Ensembl ID: ENSCJAG00000016248
• Aliases: None
• Description: gem (nuclear organelle) associated protein 2 [Source:HGNC Symbol;Acc:10884]

Sequence

>retro_cjac_2630
ATCGAAGCAGCTCAATGTCCAGATGTTGTGGTAGCTCAAATTGACCCAAAGAAGTTGAAAAGGAAGCAAAGTGTGAATAT
TTCTCTTTCAGGATGCCAACCCGCCCCTGAAGGTTATTCACCAACACTTCACTGGCAACAGCAACCAGTGGCACGGTTTT
CAACTGTTCGACAGAATGTGAACAAACATAGAAGTCACTGGAAAACACAACAGTTTGACAGTAATGTGACCAGGCCAAAA
TCTGAAGATGAAGAAGCCTGGAAGAAATTTTGTCTGGGTGAAAAGTTATGTGCTGATGGTGCTGTTGGACCAGCCACAAA
TGAAAGTCCTGGAATAGATTATGTACAAATTGGTTTTCCTCCCTTGCTTAGTATTGTTAGCAGAATGAATCAGGCAACAA
TAACTAGTGTCTTGGAATATCTGAGTAATTGGTTTGGAAAAGAGACTTTACTCCGAAATTGGGAAGATGACTTTATGCTT
TATTGGCTTGTCTTGAAAAGCCTTTATTATCTGAGGCTCATTCACTGATTCGGCAGCTTGCAAGAAGGTGCTCTGAAGTG
AGGCTCTTAGTGGATAGCAAAGATGATGAGAGGGTTCCTGCTCTGAATTTATTAATCTGCTTGGTTAGCAGGTATTTTGA
CCAGCATGATTTAGGTGATGAGCCATCT

Alignment

ORF - retro_cjac_2630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 80.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IEAAQCPDVVVAQIDPKKLKRKQSVNISLSGCQPAPEGYSPTLQWQQQQVAQFSTVRQNVNKHRSHWKSQ
          IEAAQCPDVVVAQIDPKKLKRKQSVNISLSGCQPAPEGYSPTL.WQQQ.VA.FSTVRQNVNKHRSHWK.Q
Retrocopy IEAAQCPDVVVAQIDPKKLKRKQSVNISLSGCQPAPEGYSPTLHWQQQPVARFSTVRQNVNKHRSHWKTQ

Parental  QLDSNVTMPKSEDEEGWKKFCLGEKLCADGAVGPATNESPGIDYVQIGFPPLLSIVSRMNQATITSVLEY
          Q.DSNVT.PKSEDEE.WKKFCLGEKLCADGAVGPATNESPGIDYVQIGFPPLLSIVSRMNQATITSVLEY
Retrocopy QFDSNVTRPKSEDEEAWKKFCLGEKLCADGAVGPATNESPGIDYVQIGFPPLLSIVSRMNQATITSVLEY

Parental  LSNWFG-DRDFTPELGRWLYALLACLEKPLLPEAHSLIRQLARRCSEVRLLVDSKDDERVPALNLLICLV
          LSNWFG..RDFTP.LGR.LYALLACLEKPLL.EAHSLIRQLARRCSEVRLLVDSKDDERVPALNLLICLV
Retrocopy LSNWFG<KRDFTPKLGR*LYALLACLEKPLLSEAHSLIRQLARRCSEVRLLVDSKDDERVPALNLLICLV

Parental  SRYFDQRDLADEPS
          SRYFDQ.DL.DEPS
Retrocopy SRYFDQHDLGDEPS

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	0.16 RPM	3.95 RPM
SRP051959_heart	0.02 RPM	5.56 RPM
SRP051959_kidney	0.00 RPM	4.95 RPM
SRP051959_liver	0.02 RPM	4.20 RPM
SRP051959_lung	0.05 RPM	4.78 RPM
SRP051959_lymph_node	0.02 RPM	5.50 RPM
SRP051959_skeletal_muscle	0.02 RPM	10.94 RPM
SRP051959_spleen	0.06 RPM	4.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2630 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2630 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016248	1 retrocopy	retro_cjac_2630 ,
Dasypus novemcinctus	ENSDNOG00000018278	1 retrocopy	retro_dnov_1040,
Homo sapiens	ENSG00000092208	1 retrocopy	retro_hsap_455,
Gorilla gorilla	ENSGGOG00000016691	2 retrocopies	retro_ggor_1844, retro_ggor_438,
Microcebus murinus	ENSMICG00000004811	1 retrocopy	retro_mmur_1221,
Myotis lucifugus	ENSMLUG00000002619	1 retrocopy	retro_mluc_1005,
Mus musculus	ENSMUSG00000060121	1 retrocopy	retro_mmus_354,
Pongo abelii	ENSPPYG00000005764	1 retrocopy	retro_pabe_278,
Pan troglodytes	ENSPTRG00000006291	1 retrocopy	retro_ptro_342,