RetrogeneDB ID: retro_cjac_4038

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:1385898..1386527(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013775
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSCJAG00000020554
• Aliases: None
• Description: None

Sequence

>retro_cjac_4038
GCACCTCCAGGTGTCTGCACAAAGACCCAGGACCCTGCCACAGCCTCCAACATCCCTGACATTCTTGAGATCATGTTCAA
AACAGGGATCCTGCGAAGGTAACCAATGTCAAGGATGGTGCCACCCACCAGACCTCCTTGGAGCTCTTCGTGTACCTGAA
CAAAGTCTTGGGAAAGCATGGCCTGCGCCGTATTGTGGAGAACCATTTCACTGGGATGAAGTCCTGAGGCATCTATGAGA
CCCCAGCAGGTGCCATTCTTTACGACGGTCATTTAGACATCAAGGCCTTCACCATGGATTGGGAAGTGGGCAAAATTAAA
CAATGTCTGTGCTTGAAATTTACTGAGCTGCTGTACACTGGTTTCTGGCACAGCACTGACTGTAAATTTATTCACCACTG
TATCGCCAAGTCCCAGGAGTGAGTGGAAGGGAAAGTGCAGGTGTCCATCTTCAAGAGCCAGGTGTACATCCTAGGCCAAA
ATTCCCCACTGTGTCTCTACAACGAGGAGGAACTGGTGAGCGTGAACATGCAGGGTGACTATGAGCCACTTGATGCCACC
AGTTTCATCAACATCAGTTCCCTCAGGCCAAAGGAATATCGTCATCTCCAGAGGAAGGTCACTGCCAAA

Alignment

ORF - retro_cjac_4038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.12 %
• Parental protein coverage: 51.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APPGLYTKTQDPAKAPNTPDILEIEFKKGV-PVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVE
          APPG..TKTQDPA.A.N.PDILEI.FK.G..P.KVTNVKDG.THQTSLELF.YLN.V.GKHG..RI..VE
Retrocopy APPGVCTKTQDPATASNIPDILEIMFKTGI<PAKVTNVKDGATHQTSLELFVYLNKVLGKHGLRRI--VE

Parental  NRFIGMKSRGIYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAK
          N.F.GMKS.GIYETPAG.ILY..HLDI.AFTMD.EV.KIKQ.L.LKF.EL.YTGFWHS..C.F..HCIAK
Retrocopy NHFTGMKS*GIYETPAGAILYDGHLDIKAFTMDWEVGKIKQCLCLKFTELLYTGFWHSTDCKFIHHCIAK

Parental  SQERVEGKVQVSVLKGQVYILGRESPLSLYN-EELVSMNVQGDYEPIDATGFININSLRLKEYHRLQSKV
          SQE.VEGKVQVS..K.QVYILG..SPL.LYN.EELVS.N.QGDYEP.DAT.FINI.SLR.KEY..LQ.KV
Retrocopy SQE*VEGKVQVSIFKSQVYILGQNSPLCLYNEEELVSVNMQGDYEPLDATSFINISSLRPKEYRHLQRKV

Parental  TAK
          TAK
Retrocopy TAK

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	51.56 RPM
SRP051959_heart	0.00 RPM	15.54 RPM
SRP051959_kidney	0.00 RPM	351.05 RPM
SRP051959_liver	0.00 RPM	707.59 RPM
SRP051959_lung	0.00 RPM	14.62 RPM
SRP051959_lymph_node	0.00 RPM	4.82 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.01 RPM
SRP051959_spleen	0.00 RPM	10.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4038 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4038 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038 , retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,