RetrogeneDB ID: retro_cjac_2372

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:118389056..118390075(+)
• Located in intron of: ENSCJAG00000004178

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRD7
• Ensembl ID: ENSCJAG00000001832
• Aliases: None
• Description: None

Sequence

>retro_cjac_2372
GAGAGAATGAATCAATGGATGAGACAACTGCAGAGAAAAGAGCCAAATGCTTTATTTTCATTTACTGTGACTGATTTTAT
TGCTCCTGGCTACTCCATGATCATTAAACACCCAATGGATCTTAGTACCATGAAAGAAAAGATCAAGAACAATGACTATC
AGTCCACAGAAGAACTAAAGGATAACTTCGAACTAATAGGTACTAATGCCATGACTTACGACAAACAAGAGACAACTTAT
TATAAAGCTGCAAAGAAGCTGTTGCACTCAGGGATGAAAGTTTTTAGCCAGGAAAGAATTAAGAGCCTGAAGCAGAGCAC
AGACTTCACAGATGACTTGCAAAAAACTTGAAAGCAGAAAGACAGAACAACATCTCATAGAGTGGAGAGGATAGAGATTA
CTGGCTGAGAGAGGACTCTGGAGATGCCGAAGCACAAGACTTCAAGAGTCTCAGCAATGAAAATAAAAAGAAAGATGAAG
ATATGCTTAAAGATAAGTTTAAAAACAATAATTTAGAGAGAGCAGGCACAGCTTGACCGCACTGTGAAGGAATCTAGAGG
AAAGCTGACCGGTAGCTTGTTAACAGTCAATGGGAATTTGAAAGAAGAAAACCAAATGGAACGAGAAGATTGGAACTTCT
CCATCCTGTGGATCCCACTGTAGGAAAGCCAGGCTAATGCCCTGTGAGACTGGGAATGACAACTGGAAGACTTCAGTCTG
AAATGAATACTTTGCATGGGTTCAAAGAGGATAAAAGGTACAAAGTAACCACAATGTTATATTTCAATTATGGACCCTAG
AGTTCCTATGTACCATATTATGACTACAAGTTTACAAATATCAGCAAGGATGATTTAGATTGAATCTATTCAACCTATGG
GGAAGAATCTGATCTTTGAAGCAATTTTAGCATCTAGGAATTTTTGACCACATGCCAAGATTATCCATATATTATGACAG
ATAGCTGGATGTTATAACAAAAGGAGGGTATTCCCAGGGTCCTGGAGTTGGAGATGTCT

Alignment

ORF - retro_cjac_2372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 53.0 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNA
          E..NQ.MRQLQRK.P.A.FSF.VTDFIAPGYSMIIKHPMD.STMKEKIKNNDYQS.EELKDNF.L..TNA
Retrocopy ERMNQWMRQLQRKEPNALFSFTVTDFIAPGYSMIIKHPMDLSTMKEKIKNNDYQSTEELKDNFELIGTNA

Parental  MIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSIDFMADLQKTRKQKDRTDTSQ-SGEDGGCWPRER
          M.Y.K.ET.YYKAAKKLLHSGMK..SQERI.SLKQS.DF..DLQKT.KQKDRT.....SGED...W.RE.
Retrocopy MTYDKQETTYYKAAKKLLHSGMKVFSQERIKSLKQSTDFTDDLQKT*KQKDRTTSHR<SGEDRDYWLRE-

Parental  EDSGDAEAQAFKSPSKENKKKDKDMLEDKFRSNN-LEREQEQLDRIVRESGGKLT-RRLVNSQCEFERRK
          .DSGDAEAQ.FKS.S.ENKKKD.DML.DKF..NN...REQ.QLDR.V.ES.GKLT.R.LVNSQ.EFERRK
Retrocopy -DSGDAEAQDFKSLSNENKKKDEDMLKDKFK-NN>I*REQAQLDRTVKESRGKLT<R*LVNSQWEFERRK

Parental  PDGTTTLGLLHPVDPIVGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYSSYAPHY
          P.GT..L.LLHPVDP.VG.PG.CPVRLGMTTGRLQS..NTL.GFKEDKR.KVT..LY.NYGP.SSY.P.Y
Retrocopy PNGTRRLELLHPVDPTVGKPG*CPVRLGMTTGRLQSEMNTLHGFKEDKRYKVTTMLYFNYGP*SSYVPYY

Parental  DSTFANISKDDSDLIYSTYGEDSDLPSDFSIHEFLATCQDYPYVMADSLLDVLTKGGHSRTLQELEMS
          D..F.NISKDD.D.IYSTYGE.SDL.S.FSI.EFL.TCQDYPY.M.DS......K.G..R.L.ELEMS
Retrocopy DYKFTNISKDDLD*IYSTYGEESDL*SNFSI*EFLTTCQDYPYIMTDSWM-L*QKEGIPRVL-ELEMS

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	0.80 RPM	33.10 RPM
SRP051959_heart	3.35 RPM	27.33 RPM
SRP051959_kidney	0.84 RPM	37.10 RPM
SRP051959_liver	0.26 RPM	21.83 RPM
SRP051959_lung	2.46 RPM	48.51 RPM
SRP051959_lymph_node	2.19 RPM	57.94 RPM
SRP051959_skeletal_muscle	1.11 RPM	23.56 RPM
SRP051959_spleen	1.45 RPM	46.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2372 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2372 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2384

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009355	1 retrocopy	retro_chof_2431,
Callithrix jacchus	ENSCJAG00000001832	1 retrocopy	retro_cjac_2372 ,
Homo sapiens	ENSG00000166164	2 retrocopies	retro_hsap_2723, retro_hsap_3507,
Gorilla gorilla	ENSGGOG00000014824	2 retrocopies	retro_ggor_1895, retro_ggor_2372,
Monodelphis domestica	ENSMODG00000013057	1 retrocopy	retro_mdom_152,
Otolemur garnettii	ENSOGAG00000011289	2 retrocopies	retro_ogar_326, retro_ogar_438,
Pan troglodytes	ENSPTRG00000008103	3 retrocopies	retro_ptro_1840, retro_ptro_2379, retro_ptro_2384,