RetrogeneDB ID: retro_cjac_380

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:7639718..7640423(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA8
• Ensembl ID: ENSCJAG00000002008
• Aliases: None
• Description: cell division cycle associated 8 [Source:HGNC Symbol;Acc:14629]

Sequence

>retro_cjac_380
AAGAACCTCCTCAAGGAGGTGGATAACCTCTACAACATCAAGATGCTGTGACTTCCCAAGGCGCTGCATGAGATGAGCTG
GCTCAACTACTTTGCCCTTGGAGGAAACAAGCAGGCCCTGGAAGAGGCAGCAACAGCTGACCTGGATATCACCGAAACAA
ACAAACTAACAGCAGAAGCTATTCAGACATCCCTGAAATCGGCCAAAACATGAAAGGTAATACAACTAGACAAAATGATA
GTAGAAAAGAAGAAGAAACAAATAAACATAAGAATCTTCAAACTGCAAGAGTCAAAAGGTGTCCTCCATCCAAGAAGAGA
ACTCAGTCCGTACAAGGAAAAGGCAAAAGGAAAAGGTCAAGCTGTGCTAACACTGTTACCCCAGCGTGGGCTGATTGAAG
GCGTCCATGGTGAAACCAACTCCAGGCCTGACACCCAGGTTTGACTCGAGGGTCTTCAAGACCCCGGCCTGCACACTCCG
GCAGCAGGAGAGCGGATTTCCTACATCTCAGGGAATGGCAGCCCTCTTGCAGGCAGCAATGAGATCTTCCTCACTGTGCT
AGTGGGCAGCAGAGAGAGCCTGCGATTATTGGCCAGTGACTTGCAGGGGCACAGTATGGCTCAGCTGGATCCAGAGGCCC
TGAGAAACACTAAGAAGCTCTCCAACCATCTCACCCAAATCTGCAGCAGCATACGGACCCACAAA

Alignment

ORF - retro_cjac_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.16 %
• Parental protein coverage: 84.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QNLLKEVDNLYNIEILRLPKALREMNWLDYFALGGNKQALEEAATADLDITEINKLTAEAIQTPLKSAKT
          .NLLKEVDNLYNI..L.LPKAL.EM.WL.YFALGGNKQALEEAATADLDITE.NKLTAEAIQT.LKSAKT
Retrocopy KNLLKEVDNLYNIKML*LPKALHEMSWLNYFALGGNKQALEEAATADLDITETNKLTAEAIQTSLKSAKT

Parental  RKVIQVDEMIVE-EEEEEEENKHKNLQTARVKRCPPSKKRTQSVQGKGKRKRSSRANIVTPA-MGRLEAS
          .KVIQ.D.MIVE..EEE.....HKNLQTARVKRCPPSKKRTQSVQGKGKRKRSS.AN.VTPA..G.L.AS
Retrocopy *KVIQLDKMIVE<KEEETNK--HKNLQTARVKRCPPSKKRTQSVQGKGKRKRSSCANTVTPA<VG*LKAS

Parental  MVKPTPGLTPRFDSRVFKT-PGLRTPAAGERIYNISGNGSPLADSKEIFLTVPVGGGENLRLLASDLQRH
          MVKPTPGLTPRFDSRVFKT.PGL.TPAAGERI..ISGNGSPLA.S.EIFLTV.VG..E.LRLLASDLQ.H
Retrocopy MVKPTPGLTPRFDSRVFKT<PGLHTPAAGERISYISGNGSPLAGSNEIFLTVLVGSRESLRLLASDLQGH

Parental  SIAQLDPEALGNIKKLSNRLAQICSSIQTRK
          S.AQLDPEAL.N.KKLSN.L.QICSSI.T.K
Retrocopy SMAQLDPEALRNTKKLSNHLTQICSSIRTHK

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	0.07 RPM	12.60 RPM
SRP051959_heart	0.07 RPM	0.07 RPM
SRP051959_kidney	0.49 RPM	0.47 RPM
SRP051959_liver	0.04 RPM	0.35 RPM
SRP051959_lung	0.37 RPM	1.22 RPM
SRP051959_lymph_node	0.00 RPM	4.31 RPM
SRP051959_skeletal_muscle	0.24 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	2.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_380 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_380 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028556	2 retrocopies	retro_acar_139, retro_acar_200,
Choloepus hoffmanni	ENSCHOG00000004959	1 retrocopy	retro_chof_679,
Callithrix jacchus	ENSCJAG00000002008	1 retrocopy	retro_cjac_380 ,
Homo sapiens	ENSG00000134690	1 retrocopy	retro_hsap_4052,
Gorilla gorilla	ENSGGOG00000007719	2 retrocopies	retro_ggor_2594, retro_ggor_2721,
Microcebus murinus	ENSMICG00000011926	1 retrocopy	retro_mmur_1589,
Macaca mulatta	ENSMMUG00000014340	2 retrocopies	retro_mmul_1611, retro_mmul_2339,
Nomascus leucogenys	ENSNLEG00000011630	2 retrocopies	retro_nleu_2803, retro_nleu_3006,
Pongo abelii	ENSPPYG00000001526	2 retrocopies	retro_pabe_3224, retro_pabe_3234,
Pan troglodytes	ENSPTRG00000000552	3 retrocopies	retro_ptro_2531, retro_ptro_2533, retro_ptro_2746,