RetrogeneDB ID: retro_cjac_557

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:79916748..79917809(-)
• Located in intron of: ENSCJAG00000012598

Retrocopy information

• Ensembl ID: ENSCJAG00000012618
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DND1
• Ensembl ID: ENSCJAG00000016345
• Aliases: None
• Description: dead end homolog 1 (zebrafish) [Source:HGNC Symbol;Acc:23799]

Sequence

>retro_cjac_557
ATGCAGTCCAAGCGGGATTGTGAGCTGTGGTGTGAGAGGGTGAATTCAGAAAACAAGGCAGCGCTGGAGGCTTGGGTCAG
CGAGACAGGCATCCGCCTGGTGCAGGTGAATGGGCAGAGGAATATGGCAGGCCACCCCCAGGCTGGGTGGGCAGGCTGCT
GCCAGCCGGATCAGAGGTATTCATCGGGTGGCTGCCCCAGGACGTGTACGAGCACCAGCTTATCCCACTGTTCCAGCGCG
TGGGCCGCCTCTTCGAGTTCCGCCTGATGATGACCTTCAGCGGCCTGAACCGCGGCTTTGCCTATGCCAGCTACAGCTCG
TGGCGCGGCGCTCAGGCCGCCATTGCCACGCTGCACAACTACCCGCTGCAGCCGTCTTGCACGCTGCTCATGTGCCGCAG
CATCGAGAAGTGTGAGCTGAGCGTGGACTGCCTGCTGCCGAATCTGACCTGCCGCGCACTGTTACTCGTGTTGCAGTCGC
TGGGTCCTGGCCTCCAGGAGGAGCGGGTGCTGCCCAGCCCTGGACCGCTGCCCGGGCAGATCGCTCTGCTCAAATTCAGC
TCGCACCGGACCGCTACCCTGGCCAAAAAGGTGCTGGTGGAAGGGCAATCACACCTCTGTGGAGAGCCTGTCGCTGTGGA
TTGGCTCAAGCCAGACCTGAAGCAGCGACCCCGCCAGCAGCTTGTGGGTCCCTCCTTGTGGTCCCCACAGCCAGAAGGCA
GCCAGTTGGCCTTGGCAAGGGACAAGTTAGGGTCCCAAGGGGCTCGAGCTACCCTGCAGTTGCTGTGCCAACGAATGAAG
CTGGGGAGCCCTGTGTTCCTCACCAAGTGTTTGGGCACCGGGCCTGCTGGCTGGCACCGCTTCTGGTACCAGGTCGTGAT
CCCTGGGCATCCAGTACCCTTCAGTGGCCTAATCTGGGTTGTGCTGACCCTAGATGGGCAGGATGGGCATGAGGTGGCCA
AGGATGCTGTGTCTGCACAGCTGCAGCAGCAGGCACTCACTGAGTCCCGGGCCAGCCTCCTGTGGTCTGCTGGAGCTGAG
GCAGGTACCATGGTTAGACAG

Alignment

ORF - retro_cjac_557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSKRDCELWCERVNPENKAALEAWVRETGIRLVQVNGQR-KYGGPPPGWVGRPPPAGSEVFIGRLPQDV
          MQSKRDCELWCERVN.ENKAALEAWV.ETGIRLVQVNGQR..YG.PPPGWVGR..PAGSEVFIG.LPQDV
Retrocopy MQSKRDCELWCERVNSENKAALEAWVSETGIRLVQVNGQR<EYGRPPPGWVGRLLPAGSEVFIGWLPQDV

Parental  YEHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQAAIATLHNHPLRPSCTLLVCRSTEKCE
          YEHQLIPLFQRVGRL.EFRLMMTFSGLNRGFAYA.YSS.RGAQAAIATLHN.PL.PSCTLL.CRS.EKCE
Retrocopy YEHQLIPLFQRVGRLFEFRLMMTFSGLNRGFAYASYSSWRGAQAAIATLHNYPLQPSCTLLMCRSIEKCE

Parental  LSVDGLPPNLTRRALLLALQPLGPGLQEARLLPSPGPAAGQIALLKFSSHRAAALAKKALVEGQSHLCGE
          LSVD.L.PNLT.RALLL.LQ.LGPGLQE.R.LPSPGP..GQIALLKFSSHR.A.LAKK.LVEGQSHLCGE
Retrocopy LSVDCLLPNLTCRALLLVLQSLGPGLQEERVLPSPGPLPGQIALLKFSSHRTATLAKKVLVEGQSHLCGE

Parental  PVAVEWLKPDLKQRLRQQLVGPSLRSPQPEGSQLALARDKLGSQGARATLQLLCQRMKLGSPVFLTKCLG
          PVAV.WLKPDLKQR.RQQLVGPSL.SPQPEGSQLALARDKLGSQGARATLQLLCQRMKLGSPVFLTKCLG
Retrocopy PVAVDWLKPDLKQRPRQQLVGPSLWSPQPEGSQLALARDKLGSQGARATLQLLCQRMKLGSPVFLTKCLG

Parental  TGPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGQDGHEVAKDAVSAQL-LQVLTESGASLLWSAGAEAR
          TGPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGQDGHEVAKDAVSAQL..Q.LTES.ASLLWSAGAEA.
Retrocopy TGPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGQDGHEVAKDAVSAQLQQQALTESRASLLWSAGAEAG

Parental  TMVRQ
          TMVRQ
Retrocopy TMVRQ

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	0.47 RPM	1.24 RPM
SRP051959_heart	0.32 RPM	0.84 RPM
SRP051959_kidney	0.33 RPM	1.29 RPM
SRP051959_liver	0.35 RPM	1.67 RPM
SRP051959_lung	0.49 RPM	1.40 RPM
SRP051959_lymph_node	0.43 RPM	2.83 RPM
SRP051959_skeletal_muscle	0.09 RPM	1.40 RPM
SRP051959_spleen	0.40 RPM	1.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_557 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_557 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016345	1 retrocopy	retro_cjac_557 ,
Homo sapiens	ENSG00000256453	1 retrocopy	retro_hsap_1760,
Macropus eugenii	ENSMEUG00000016276	2 retrocopies	retro_meug_1326, retro_meug_614,
Mus musculus	ENSMUSG00000044595	1 retrocopy	retro_mmus_2548,
Pongo abelii	ENSPPYG00000015863	1 retrocopy	retro_pabe_1502,
Rattus norvegicus	ENSRNOG00000016894	1 retrocopy	retro_rnor_2782,