RetrogeneDB ID: retro_cjac_3225

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:62532324..62532792(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001285
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCDC12
• Ensembl ID: ENSCJAG00000002280
• Aliases: None
• Description: coiled-coil domain containing 12 [Source:HGNC Symbol;Acc:28332]

Sequence

>retro_cjac_3225
CAACAGAGAAAAAAAGGCGTGGTGTCGGCAGGCAAGATGGAGCCGACTGTGGCCGGTGTGGGCCGGCTAGAGGAAGAGGC
ACTGCGGCGAAAGGAATGGCTGAAGGCCCTACGGGAGAAAAACGGGCGCAAGGACAAGGAAGATGGGGAGCCAAAGACCA
AGCAACTTAGAGAAGAGGAGGAAGAAGGCGAGAAGCACAGGGAACTTAGACTGCGGAACTATGTCCCAGAGGATGAGGAC
CTGAAGAAGAGGAGGGTGCCCCAGGCCAAACCGGTTGCCGTGGAAGAGAAGGTGAAGGAGCAGCTGGAGGCTGCCAAGCC
CGAGCCCGTCATCGAGGAGGTGGATCTGGCCAACCTCGCTCCTCGGAATCCTGACTGGGACCTCAAGAGAGATGTGGCCA
AGAAGCTGGAGAAACTGAAAAAGACGACTCAGAGGGCCATTGCCGAGCTGATCCGTGAAAGACTGAAA

Alignment

ORF - retro_cjac_3225 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 87.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDGRKGGASAGKMEPTVAGVGRLEEEALRRKERLKALREKTGRKDKEDGEPKTKQLREEEEEGEKHRELR
          Q...KG..SAGKMEPTVAGVGRLEEEALRRKE.LKALREK.GRKDKEDGEPKTKQLREEEEEGEKHRELR
Retrocopy QQRKKGVVSAGKMEPTVAGVGRLEEEALRRKEWLKALREKNGRKDKEDGEPKTKQLREEEEEGEKHRELR

Parental  LRNYVPEDEDLKKRRVPQAKPVAVEEKVKEQLEAAKPEPVIEEVDLANLAPRKPDWDLKRDVAKKLEKLK
          LRNYVPEDEDLKKRRVPQAKPVAVEEKVKEQLEAAKPEPVIEEVDLANLAPR.PDWDLKRDVAKKLEKLK
Retrocopy LRNYVPEDEDLKKRRVPQAKPVAVEEKVKEQLEAAKPEPVIEEVDLANLAPRNPDWDLKRDVAKKLEKLK

Parental  KRTQRAIAELIRERLK
          K.TQRAIAELIRERLK
Retrocopy KTTQRAIAELIRERLK

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	6.01 RPM
SRP051959_heart	0.05 RPM	9.31 RPM
SRP051959_kidney	0.04 RPM	8.03 RPM
SRP051959_liver	0.00 RPM	6.15 RPM
SRP051959_lung	0.08 RPM	9.34 RPM
SRP051959_lymph_node	0.00 RPM	10.84 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.26 RPM
SRP051959_spleen	0.02 RPM	7.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3225 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3225 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225 ,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251,