RetrogeneDB ID: retro_cjac_2754

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:116831614..116832737(+)
• Located in intron of: ENSCJAG00000004558

Retrocopy information

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

Parental gene information

• Parental gene symbol: DMAP1
• Ensembl ID: ENSCJAG00000003922
• Aliases: None
• Description: None

Sequence

>retro_cjac_2754
TGGAAGTGGATGCCATTCACCAACCTGGCCCGCAAGGATGGAGCAATGTTCTTCCACTGGCGATGTACAGCGGAGGAGGG
CAAGGACTACCCCTTTGCCAGGTTAAATAAGGCTGTGCAGGTACCTGTGTACTCAGAGCAGGAGTACCGGCTTTATCTCC
ATGATGATGCTTGGACTAAGGCAGAAACTGACCACCCCTTTGACCTCAGCTGCCGCTTTGACCTGCGTTTTGTTGTTATC
CATGACCGGTATGACCACCAGCAGTTCAAGAAGCGTTCTGTGGAAGACTTGAAGGAATGGTACTACCACATCTGTGCTAA
GCTTGCCAATGTGTGGGCTGTGCCAGGCACAGACCTTAAGATACCAGTATTTGATGCTGGGCATGAATGACGACGGAAGG
AACAGCTCAAGTGGCTGTACAACCGGACCCCAGAGCAGGGGGCAGAGGAGGAGTAAGTACCTGCTGCAGGAGCTGCGCAA
GATCGAGGCCCGGAAGAAGGAGCGGGAGAAACGCAGCCAGGACCTGCAGAAGCTGATCACAGCGGCAGATACCACTGCAG
AGCAGAGGCGCACGGAACGCAAGGCCCCCAAGAAGAAGCTACCACAGAAAAAAGAGGCTGAGAAGCCGGCTGTTCGTGAG
ACTGCAGGCATCAAATTTCCAGACTTCAAGTCTGCAGGTGTCACGCTGCGGAGCCAACAGATGAAGCTGCCAAGCTCTGT
GGGACAGAAGAAGATCAAGGCCCTGGAACAGATGCTGCGGGAGCTTGGTGTGGAGCTGAGCCCGATACCTACGGGGGAGC
TGGTGCACATGTTCAACGAGCTGCGAAGTGACCTGGTGCTGCTCTACGAGCTCAAGCAGGCCTGTGCCAACTGCAAGTAT
GAGCTGCAGATGCTGTGGCACCGTCATGAGGCACTGGCCCGGACTGGTGTGCTGGGGGGCCCTGCCACACCAGCATCAGG
CCCAGGCCCGGCCTCCGCTGAGCCAGCAGTGACCGAACCCGGACTTGGCCCTGACCCCAAGGACACCATCATTGATGTGG
TGGGTGCACCCCTCACGCCCAATTCGAGAAAGCGATGGGAGTCAGCCTCCAGCTCATCTTCTGTGAAGAAAGCCAAGAAG
CCG

Alignment

ORF - retro_cjac_2754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.07 %
• Parental protein coverage: 79.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WKWMPFTNPARKDGAMFFHWRRAAEEGKDYPFARFNKTVQVPVYSEQEYQLYLHDDAWTKAETDHLFDLS
          WKWMPFTN.ARKDGAMFFHWR..AEEGKDYPFAR.NK.VQVPVYSEQEY.LYLHDDAWTKAETDH.FDLS
Retrocopy WKWMPFTNLARKDGAMFFHWRCTAEEGKDYPFARLNKAVQVPVYSEQEYRLYLHDDAWTKAETDHPFDLS

Parental  RRFDLRFVVIHDRYDHQQFKKRSVEDLKERYYHICAKLANVRAVPGTDLKIPVFDAGHERRRKEQLERLY
          .RFDLRFVVIHDRYDHQQFKKRSVEDLKE.YYHICAKLANV.AVPGTDLKIPVFDAGHE.RRKEQL..LY
Retrocopy CRFDLRFVVIHDRYDHQQFKKRSVEDLKEWYYHICAKLANVWAVPGTDLKIPVFDAGHE*RRKEQLKWLY

Parental  NRTPEQVA-EE-EYLLQELRKIEARKKEREKRSQDLQKLITAADTTAEQRRTERKAPKKKLPQKKEAEKP
          NRTPEQ.A.EE..YLLQELRKIEARKKEREKRSQDLQKLITAADTTAEQRRTERKAPKKKLPQKKEAEKP
Retrocopy NRTPEQGAEEE>KYLLQELRKIEARKKEREKRSQDLQKLITAADTTAEQRRTERKAPKKKLPQKKEAEKP

Parental  AVPETAGIKFPDFKSAGVTLRSQRMKLPSSVGQKKIKALEQMLLELGVELSPTPTEELVHMFNELRSDLV
          AV.ETAGIKFPDFKSAGVTLRSQ.MKLPSSVGQKKIKALEQML.ELGVELSP.PT.ELVHMFNELRSDLV
Retrocopy AVRETAGIKFPDFKSAGVTLRSQQMKLPSSVGQKKIKALEQMLRELGVELSPIPTGELVHMFNELRSDLV

Parental  LLYELKQACANCEYELQMLRHRHEALARAGVLGGPATPASGPGPASAEPAVTEPGLGPDPKDTIIDVVGA
          LLYELKQACANC.YELQML.HRHEALAR.GVLGGPATPASGPGPASAEPAVTEPGLGPDPKDTIIDVVGA
Retrocopy LLYELKQACANCKYELQMLWHRHEALARTGVLGGPATPASGPGPASAEPAVTEPGLGPDPKDTIIDVVGA

Parental  PLTPNSRKRRESASSSSSVKKAKKP
          PLTPNSRKR.ESASSSSSVKKAKKP
Retrocopy PLTPNSRKRWESASSSSSVKKAKKP

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	0.27 RPM	5.41 RPM
SRP051959_heart	0.11 RPM	8.16 RPM
SRP051959_kidney	0.13 RPM	6.77 RPM
SRP051959_liver	0.13 RPM	6.52 RPM
SRP051959_lung	0.62 RPM	8.39 RPM
SRP051959_lymph_node	1.16 RPM	7.33 RPM
SRP051959_skeletal_muscle	0.20 RPM	14.41 RPM
SRP051959_spleen	0.40 RPM	6.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2754 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2754 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2754 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003922	1 retrocopy	retro_cjac_2754 ,
Mus musculus	ENSMUSG00000009640	1 retrocopy	retro_mmus_1744,
Rattus norvegicus	ENSRNOG00000019407	4 retrocopies	retro_rnor_2428, retro_rnor_2504, retro_rnor_2507, retro_rnor_2940,