RetrogeneDB ID: retro_cjac_3292

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:37545392..37545776(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C20orf27
• Ensembl ID: ENSCJAG00000021194
• Aliases: None
• Description: chromosome 20 open reading frame 27 [Source:HGNC Symbol;Acc:15873]

Sequence

>retro_cjac_3292
ATGGGTGCAGCCAATAAGGGCAACAGTCCAGATTCTGAGTATCTGCTTTACAACGGGCCAGGATACAGAGGGCTGCCAGA
ACCACATTTGGTTTGATGAGAAGCTGCATGACTCAGTGGTCATGGTCACCCAAGAGAGTGACAACAGCTTTCTGGTCAAG
GTTTGGCTTCCTGAAGATCCTGCACAGGTATGAGATTACCTTCGCTCTGCCCCAGTACACAGGCTGAGCCAAGATGTCCG
TCAGTCACCTGTCCCCAGCCTGCACCTCAAGCTTCTCATCGTACCTGTCCATGAAGGTTATAGTACCAAGTGCAAGTACT
TGGCCACAAAGAGGGTATCTTCAAAGAGGGGAGGCTGCTAGCCTGGGAAGGTGGCGCTGGCACC

Alignment

ORF - retro_cjac_3292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.11 %
• Parental protein coverage: 74.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAAANK-GNKPR-VRSIRFAAGHDAEGSHSHVHFDEKLHDSVVMVTQESDSSFLVKV-GFLKILHRYEIT
          M.AANK.G...R...SI.F..G.D.EG...H..FDEKLHDSVVMVTQESD.SFLVKV.GFLKILHRYEIT
Retrocopy MGAANK<GQQSR<ILSICFTTGQDTEGCQNHIWFDEKLHDSVVMVTQESDNSFLVKV>GFLKILHRYEIT

Parental  FTLP-PVHRLSKDIHEAPVPSLHLKLLSIVPVPEGYSVKCEYSA-HKEGVLKEEILLACEGGTGT
          F.LP.PVHRLS.D....PVPSLHLKLL.IVPV.EGYS.KC.Y.A.HKEG..KE..LLA.EGG.GT
Retrocopy FALP<PVHRLSQDVRQSPVPSLHLKLL-IVPVHEGYSTKCKYLA<HKEGIFKEGRLLAWEGGAGT

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	2.48 RPM
SRP051959_heart	0.02 RPM	4.40 RPM
SRP051959_kidney	0.00 RPM	7.03 RPM
SRP051959_liver	0.00 RPM	6.84 RPM
SRP051959_lung	0.00 RPM	6.31 RPM
SRP051959_lymph_node	0.00 RPM	6.83 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.07 RPM
SRP051959_spleen	0.00 RPM	13.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3292 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3292 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3292 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021194	1 retrocopy	retro_cjac_3292 ,
Homo sapiens	ENSG00000101220	2 retrocopies	retro_hsap_1114, retro_hsap_1673,
Gorilla gorilla	ENSGGOG00000016987	1 retrocopy	retro_ggor_871,
Macaca mulatta	ENSMMUG00000022079	1 retrocopy	retro_mmul_1578,
Nomascus leucogenys	ENSNLEG00000007653	1 retrocopy	retro_nleu_194,
Pongo abelii	ENSPPYG00000010813	1 retrocopy	retro_pabe_923,
Pan troglodytes	ENSPTRG00000013204	2 retrocopies	retro_ptro_1136, retro_ptro_685,