RetrogeneDB ID: retro_cjac_1827

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:97224384..97224948(+)
• Located in intron of: ENSCJAG00000016199

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004135
• Aliases: None
• Description: None

Sequence

>retro_cjac_1827
ATGACTAATAAAGCAGAGAAGTTTGCTGTAGAACTTGAAAACATGTTTAAATGTCCCAGGGAATCTGAGAGCCCTTCATC
TCAGAAAAGGCAGAAGATGGATTTGTTGTTAAAGAAACAATGAGCAGGAGACAGCCTTATTGGAGGCTCTGCCATGTACA
AGGAAAAGAAGCTTATGGCAGGAGATGGTATTCCAATCAGCCAGTTGGATTTTCAGTTTGATGACTTCACTGGTTTCAGC
GAAGATGGGCTGATGCAGAAACCTGGTAGAAATGCACCTGTAAAAGGAATCATTGCCAGCAACTTCTCTGGAGATGATCC
CAAAGTCACAGAAACATTCCCTTTTCCAAAAAGCCAAGAAGAAATTAATGCTGATATAAAATGTCAATAGTGAAGGAAAT
TTGACACTTTGGATGAAATGTGAAAAACTCCTGAAATTGCTTGAAGGAGTACAAAGACCTGCGGAAGTCAAGAAATTATT
TTTTGAATCCATTATCAAGGATAGCAGCAAGATTTACGAGACCAGACTTAATTTTAGCACCTTGAGAAGAAACTGGAACA
AATG

Alignment

ORF - retro_cjac_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.1 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTDKTERVAGDPETVFKRPRECDSPSYQKRQKMALLARKQGAGDGLIGGSAMSKEKKLKVGDGIPLSQC-
          MT.K.E..A...E..FK.PRE..SPS.QKRQKM.LL..KQ.AGD.LIGGSAM.KEKKL..GDGIP.SQ..
Retrocopy MTNKAEKFAVELENMFKCPRESESPSSQKRQKMDLLLKKQ*AGDSLIGGSAMYKEKKLMAGDGIPISQLD

Parental  YWIDEFIGFSKDGLMQKRDRNATVGGIITSNFSADDLKVTEILLFPKSQEKINSDIKCQ-LMKEIQHFG-
          ...D.F.GFS.DGLMQK..RNA.V.GII.SNFS.DD.KVTE...FPKSQE.IN.DIKCQ...KEI.HFG.
Retrocopy FQFDDFTGFSEDGLMQKPGRNAPVKGIIASNFSGDDPKVTETFPFPKSQEEINADIKCQ<IVKEI*HFG<

Parental  QIYEKIFKLLDGLQGPIEVKKQVFESIIKE-AARYMRGDLIP-HLEKRLEEM
          ...EK..KLL.G.Q.P.EVKK..FESIIK..AAR..R.DLI..HLEK.LE.M
Retrocopy MKCEKLLKLLEGVQRPAEVKKLFFESIIKD>AARFTRPDLIL>HLEKKLEQM

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	1.04 RPM	0.00 RPM
SRP051959_heart	0.65 RPM	0.00 RPM
SRP051959_kidney	0.71 RPM	0.02 RPM
SRP051959_liver	0.45 RPM	0.00 RPM
SRP051959_lung	1.01 RPM	0.00 RPM
SRP051959_lymph_node	1.23 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.13 RPM	0.00 RPM
SRP051959_spleen	1.09 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1827 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1827 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3362
Pan troglodytes	retro_ptro_2285
Pongo abelii	retro_pabe_2766
Macaca mulatta	retro_mmul_2100

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014436	2 retrocopies	retro_cfam_441, retro_cfam_444,
Callithrix jacchus	ENSCJAG00000004135	1 retrocopy	retro_cjac_1827 ,
Dipodomys ordii	ENSDORG00000008443	1 retrocopy	retro_dord_354,
Homo sapiens	ENSG00000242284	1 retrocopy	retro_hsap_3362,
Macaca mulatta	ENSMMUG00000021984	1 retrocopy	retro_mmul_2100,
Nomascus leucogenys	ENSNLEG00000002303	1 retrocopy	retro_nleu_961,
Pongo abelii	ENSPPYG00000020755	1 retrocopy	retro_pabe_2766,
Pan troglodytes	ENSPTRG00000041730	1 retrocopy	retro_ptro_2285,