RetrogeneDB ID: retro_cjac_2257

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:110667387..110668071(-)
• Located in intron of: ENSCJAG00000005294

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A14
• Ensembl ID: ENSCJAG00000002456
• Aliases: None
• Description: None

Sequence

>retro_cjac_2257
AAAGAAACAAAACATAGAGGGATGTTTCACCCTTTGTTTCCGGTGAAACATCCGAAAGAGGAAGGTGTATTGGCTCTGTA
TTCAGGAATTGCTCCTGCTTTGCTAAGAGAAGCATAATATGGCACCATTAAAATTGAGATATACCCAAGCTTGAAGCAAT
TATTTGTAGAACATTTAGAAGATGAAACTCTTAACATGATCTGTGGGGTAGTGTCAGGAGTGATGTCTTCCACAACAGCC
AATCTCACCTATGTTCTAAAGATTCTAATGCAGGCTCAAGGAAGGTTGTTCCAAGGGAACATGATTGGCAGATTCATCGA
TATATACCAACAGGAAGGCACTGGGGTCTGTGGAGGGGTGTGGTTCCAACTTGCTCAGCATGCTGCCGTCGTTGTGGGAG
TAGAGCTACCAGTCTATGATATTACTAAGAAGCACTTAATATTGTCAGGAATGATGGGAGACACAATTTTAACTCACTTT
GTTTCCAGCTTTACATGTGGTTTGGCTGGGGCTCTTGCCTCTAATCTGGTTGATGTGGTTTGCACTTGCATGTTGAACCA
GAGGGCAATCATGGGACATGTGGATCTCTACAAGGGCACTTTGGATGTTATTTTAAAGATGTGGAAACATGAGGGCTTTT
TTGCACTCTATAAAGAATTTTGGCCACACTGGCTTTGGCTTGGA

Alignment

ORF - retro_cjac_2257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.19 %
• Parental protein coverage: 70.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEIKYRGMFHALFRIC--KEEGVLALYSGIAPALLRQASYGTIKIGIYQSLKRLFVERLEDETLLINMIC
          KE.K.RGMFH.LF.....KEEGVLALYSGIAPALLR.A.YGTIKI.IY.SLK.LFVE.LEDETL..NMIC
Retrocopy KETKHRGMFHPLFPVKHPKEEGVLALYSGIAPALLREA*YGTIKIEIYPSLKQLFVEHLEDETL--NMIC

Parental  GVVSGVISSTIANPTDVLKIRMQAQGSLFQGSMIGSFIDIYQQEGTR-GLWRGVVPT-AQRAAIVVGVEL
          GVVSGV.SST.AN.T.VLKI.MQAQG.LFQG.MIG.FIDIYQQEGT..GLWRGVVPT.AQ.AA.VVGVEL
Retrocopy GVVSGVMSSTTANLTYVLKILMQAQGRLFQGNMIGRFIDIYQQEGTG<GLWRGVVPT>AQHAAVVVGVEL

Parental  PVYDITKKHLILSGMMGDTILTHFVSSFTCGLAGALASNPVDVVRTRMMNQRAIVGHVDLYKGTVDGILK
          PVYDITKKHLILSGMMGDTILTHFVSSFTCGLAGALASN.VDVV.T.M.NQRAI.GHVDLYKGT.D.ILK
Retrocopy PVYDITKKHLILSGMMGDTILTHFVSSFTCGLAGALASNLVDVVCTCMLNQRAIMGHVDLYKGTLDVILK

Parental  MWKHEGFFALYKGFWPNWLRLG
          MWKHEGFFALYK.FWP.WL.LG
Retrocopy MWKHEGFFALYKEFWPHWLWLG

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	0.44 RPM	2.62 RPM
SRP051959_heart	0.32 RPM	1.89 RPM
SRP051959_kidney	0.27 RPM	3.06 RPM
SRP051959_liver	0.19 RPM	1.52 RPM
SRP051959_lung	0.63 RPM	2.90 RPM
SRP051959_lymph_node	0.59 RPM	2.74 RPM
SRP051959_skeletal_muscle	0.11 RPM	1.46 RPM
SRP051959_spleen	0.80 RPM	2.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2257 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2257 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1943

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016263	1 retrocopy	retro_btau_1362,
Canis familiaris	ENSCAFG00000018766	1 retrocopy	retro_cfam_1359,
Callithrix jacchus	ENSCJAG00000002456	1 retrocopy	retro_cjac_2257 ,
Homo sapiens	ENSG00000102078	1 retrocopy	retro_hsap_2954,
Macaca mulatta	ENSMMUG00000008386	1 retrocopy	retro_mmul_1943,
Nomascus leucogenys	ENSNLEG00000015318	1 retrocopy	retro_nleu_1638,
Pongo abelii	ENSPPYG00000020715	2 retrocopies	retro_pabe_2450, retro_pabe_3595,
Pan troglodytes	ENSPTRG00000022268	1 retrocopy	retro_ptro_2048,
Tursiops truncatus	ENSTTRG00000016206	2 retrocopies	retro_ttru_1159, retro_ttru_1570,