RetrogeneDB ID: retro_cjac_2668

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:133142605..133143009(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CISD2
• Ensembl ID: ENSCJAG00000015530
• Aliases: None
• Description: CDGSH iron sulfur domain 2 [Source:HGNC Symbol;Acc:24212]

Sequence

>retro_cjac_2668
ATGGTGCTGGAGAGCGTGGCCCGCATTGTGAAGGTGCAGCTCCCCGCATATCTGAAGCGGCTCCCAGTCCCCGAAAGTAT
TACCGGGTTCGCGAGACTCACAGTTTCAGAATGGCTTCGGTTATTGCCTTTCCTTGGTGTACTTGCACTTCTTGGCTACC
TTGCAGTTCGTCCATTCCTCCCGAAGAAAAAACAACGAAGGATAGCTTGATTAATCTTAAAATACAAAAGGAAAATCCGA
AAGTAGTGAATGAAATAAACATTGAAGATTTGTGTCTTACCAAAGCAGCTTATTGTAGGTGTCGGCGTTCTAAACCGTTT
CCTGCCTGCGATGGTTCACATAATAAACACCATGAATTGACAGGGGATAATGCGGGTCCACTAATACTGAAGAAGAAAGA
AGTA

Alignment

ORF - retro_cjac_2668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLESVARIVKVQLPAYLKRLPVPESITGFARLTVSEWLRLLPFLGVLALLGYLAVRPFLLKKKQQ-KDS
          MVLESVARIVKVQLPAYLKRLPVPESITGFARLTVSEWLRLLPFLGVLALLGYLAVRPFL.KKKQ..KDS
Retrocopy MVLESVARIVKVQLPAYLKRLPVPESITGFARLTVSEWLRLLPFLGVLALLGYLAVRPFLPKKKQR<KDS

Parental  LINLKIQKENPKVVNEINIEDLCLTKAAYCRCWRSKTFPACDGSHNKHNELTGDNVGPLILKKKEV
          LINLKIQKENPKVVNEINIEDLCLTKAAYCRC.RSK.FPACDGSHNKH.ELTGDN.GPLILKKKEV
Retrocopy LINLKIQKENPKVVNEINIEDLCLTKAAYCRCRRSKPFPACDGSHNKHHELTGDNAGPLILKKKEV

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	0.09 RPM	12.98 RPM
SRP051959_heart	0.23 RPM	11.19 RPM
SRP051959_kidney	0.16 RPM	16.35 RPM
SRP051959_liver	0.04 RPM	16.72 RPM
SRP051959_lung	0.11 RPM	9.66 RPM
SRP051959_lymph_node	0.14 RPM	9.91 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.35 RPM
SRP051959_spleen	0.19 RPM	13.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2668 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2668 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010779	1 retrocopy	retro_cfam_1012,
Callithrix jacchus	ENSCJAG00000015530	1 retrocopy	retro_cjac_2668 ,
Felis catus	ENSFCAG00000028054	1 retrocopy	retro_fcat_1979,
Mus musculus	ENSMUSG00000028165	1 retrocopy	retro_mmus_2257,
Nomascus leucogenys	ENSNLEG00000026930	1 retrocopy	retro_nleu_1331,
Oryctolagus cuniculus	ENSOCUG00000013943	1 retrocopy	retro_ocun_1444,
Ictidomys tridecemlineatus	ENSSTOG00000001408	1 retrocopy	retro_itri_869,