RetrogeneDB ID: retro_cjac_2111

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:30037740..30038513(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAF1
• Ensembl ID: ENSCJAG00000021450
• Aliases: None
• Description: MAF1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24966]

Sequence

>retro_cjac_2111
ATGAAGCTGTTGGAGAACTCCAGCTTTGAGGCCATCAACTCACAGCTGACCGTGGAGACTGGAGATGCCCACATCGTCGG
CAGGATTGAGAGCTACTCATGTAAGATGGCATAGATGACAAACACACGTTCCAGCAGTTCTGCCAGGAGGGCCGGCCCCA
CATGCTGGAGGCACTCTCTCCACCCCAGACCTCAGGCCTCAGCCCCAGCAGACTCAGCAAAAGCCAAGGTGGAGAAGACG
AGGGTTCCCTCGGTGACAAGTGCAGCCGCAAGACCCTCTTCTACCTGATTGCCACACTCGATGAGTCCTTCAGGCCTGAC
TATGACTTCGGCACAGCCCGCAGCCATGAATTCAGCCGGGAGCCCAGCCTTACCTGGGTGGTGAATGCAGTCAGCTGCAG
TCTGTTCTCAGCTGTGCCGGAGGACTTCAAGGCCCTGAAACCACAGCTGTGGAACACGGTGGACGAGGAGATCTGCCTGG
CTGAATGTGACATCTACAGCGATAACCCGGACTTGCACTCAGCCCCCTTCGGGGAGGATGGTAGCCTCTGGTCCTTCAAC
TACTTCTTCTACAACTAGCGGCTCAAGCAAATTGTCTTCTTTAGCTGCCGCTCCTTCAGTGGCTCGACCTACACATCCTC
AGAGGCAGGCAATGAGCTGAACATGGAGCTGGGGGAGGAGGAGGTGGAGGAAGAAAGCAGAAGTGGAGGCAGTGGGGGTG
GGGCCGAGGAGACCAGCACCATGGAGGAGGACAGGGTCTCAGTGTTCTGTATG

Alignment

ORF - retro_cjac_2111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKLLENSSFEAINSQLTVETGDAHIIGRIESYSCKMAG-DDKHMFKQFCQEGQPHVLEALSPPQTSGLSP
          MKLLENSSFEAINSQLTVETGDAHI.GRIESYSCKMA..DDKH.F.QFCQEG.PH.LEALSPPQTSGLSP
Retrocopy MKLLENSSFEAINSQLTVETGDAHIVGRIESYSCKMA*<DDKHTFQQFCQEGRPHMLEALSPPQTSGLSP

Parental  SRLSKSQGGEDEGPLSDKCSRKTLFYLIATLNESFRPDYDFSTARSHEFSREPSLSWVVNAVNCSLFSAV
          SRLSKSQGGEDEG.L.DKCSRKTLFYLIATL.ESFRPDYDF.TARSHEFSREPSL.WVVNAV.CSLFSAV
Retrocopy SRLSKSQGGEDEGSLGDKCSRKTLFYLIATLDESFRPDYDFGTARSHEFSREPSLTWVVNAVSCSLFSAV

Parental  REDFKALKPQLWNAVDEEICLAECDIYSYNPDLDSDPFGEDGSLWSFNYFFYNKRLKRIVFFSCRSISGS
          .EDFKALKPQLWN.VDEEICLAECDIYS.NPDL.S.PFGEDGSLWSFNYFFYN.RLK.IVFFSCRS.SGS
Retrocopy PEDFKALKPQLWNTVDEEICLAECDIYSDNPDLHSAPFGEDGSLWSFNYFFYN*RLKQIVFFSCRSFSGS

Parental  TYTSSEAGNELDMELGEEEVEEESRSGGSGGGAEETSTMEEDRVPVICM
          TYTSSEAGNEL.MELGEEEVEEESRSGGSGGGAEETSTMEEDRV.V.CM
Retrocopy TYTSSEAGNELNMELGEEEVEEESRSGGSGGGAEETSTMEEDRVSVFCM

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	0.04 RPM	10.18 RPM
SRP051959_heart	0.16 RPM	24.33 RPM
SRP051959_kidney	0.09 RPM	20.74 RPM
SRP051959_liver	0.02 RPM	6.87 RPM
SRP051959_lung	0.07 RPM	20.40 RPM
SRP051959_lymph_node	0.05 RPM	18.38 RPM
SRP051959_skeletal_muscle	0.13 RPM	34.55 RPM
SRP051959_spleen	0.19 RPM	18.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2111 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021450	1 retrocopy	retro_cjac_2111 ,
Homo sapiens	ENSG00000179632	1 retrocopy	retro_hsap_2708,
Macaca mulatta	ENSMMUG00000007155	1 retrocopy	retro_mmul_1537,
Nomascus leucogenys	ENSNLEG00000010478	1 retrocopy	retro_nleu_1580,
Pongo abelii	ENSPPYG00000018963	1 retrocopy	retro_pabe_2259,
Pan troglodytes	ENSPTRG00000020681	1 retrocopy	retro_ptro_1829,