RetrogeneDB ID: retro_cjac_1085

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38425715..38426316(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP25
• Ensembl ID: ENSCJAG00000015273
• Aliases: None
• Description: Sin3A-associated protein, 25kDa [Source:HGNC Symbol;Acc:41908]

Sequence

>retro_cjac_1085
ATGACTCCTCCAGCACCCTGGGACCCCAAGTACGAAGCCAAAGCAGGGCCTCGGCTGGTGTGGGGGGTCAACTGTAGCTC
AGGAGCCTCCTTCTCAGGCCAGACGCTATGTCACCCCTTGTTCTGGCTGCTGTATGAGGCAGCCTCAGGTAGGGGTCCCC
GGCCTGTGGCCCCTGCCACAGGGCATGAGAATGGGCAGCAGGTGCACCCAGATGCAGGGTTCCTGGTGATGTGCCATGAA
GACCTCTTCTTCTCAGACCCTCTACTGCCCCTGGGACAGAGTGTCCCCTTATACCTTTTCGAGGCCCCCCAGCAGGTGAT
GAGCTCCCTGAAATGGCTGCCACCACCTCCCATAATGTCCCCCTGGGTCTTCCCCAGCCTGTAACCCTCCCCAGGCCACT
CCACCGCCTGGCTCAGTGGGCTGGAGCTGATAGCTCTCACTGGCCTGCTGCAGATGAGCCAGGGGGAATCCCAGGCCCAG
CTTCTCCTCCGCTGCTGGCACCCTAGACCCTGCCTCTGACCCAACCAGCCCCTGTGGTGGCTCCAGCAGTTCTCACAGTG
CTGACCCCTCTCTCCCACAGACCCCAGACACCCATTGTTCA

Alignment

ORF - retro_cjac_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTPLAPWDPKYEAKAGPRLVWGANCSSGASFSGRTLCHPSFWPLYEAASGRGPQPVAPATGHQNGQQAHP
          MTP.APWDPKYEAKAGPRLVWG.NCSSGASFSG.TLCHP.FW.LYEAASGRGP.PVAPATGH.NGQQ.HP
Retrocopy MTPPAPWDPKYEAKAGPRLVWGVNCSSGASFSGQTLCHPLFWLLYEAASGRGPRPVAPATGHENGQQVHP

Parental  DAGFPVMCGEDVFFSDPLLPQGQRVPLYLSEAPQQVMSSLKLLPPPSIMSPWVFPSLSPSPGCSTAWLSG
          DAGF.VMC.ED.FFSDPLLP.GQ.VPLYL.EAPQQVMSSLK.LPPP.IMSPWVFPSL.PSPG.STAWLSG
Retrocopy DAGFLVMCHEDLFFSDPLLPLGQSVPLYLFEAPQQVMSSLKWLPPPPIMSPWVFPSL*PSPGHSTAWLSG

Parental  PELIALTGLLQMSQGE-PRPSSSMAATPTAGPPDPASDPTSPCGGSSSSHGADPSLPQTPDTHCS
          .ELIALTGLLQMSQGE.PRPS.S.AA....G..DPASDPTSPCGGSSSSH.ADPSLPQTPDTHCS
Retrocopy LELIALTGLLQMSQGE>PRPSFSSAA----GTLDPASDPTSPCGGSSSSHSADPSLPQTPDTHCS

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	0.35 RPM
SRP051959_heart	0.00 RPM	0.86 RPM
SRP051959_kidney	0.02 RPM	2.00 RPM
SRP051959_liver	0.00 RPM	0.54 RPM
SRP051959_lung	0.00 RPM	3.84 RPM
SRP051959_lymph_node	0.02 RPM	6.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.68 RPM
SRP051959_spleen	0.00 RPM	3.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1085 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015273	1 retrocopy	retro_cjac_1085 ,
Homo sapiens	ENSG00000205307	1 retrocopy	retro_hsap_1362,
Gorilla gorilla	ENSGGOG00000013708	1 retrocopy	retro_ggor_1060,
Pongo abelii	ENSPPYG00000017415	1 retrocopy	retro_pabe_1129,
Pan troglodytes	ENSPTRG00000019495	1 retrocopy	retro_ptro_934,