RetrogeneDB ID: retro_cjac_2093

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:13782024..13782302(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004673
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDCD2
• Ensembl ID: ENSCJAG00000015367
• Aliases: None
• Description: NudC domain containing 2 [Source:HGNC Symbol;Acc:30535]

Sequence

>retro_cjac_2093
ATGTCGGCCCCATTTGAGGAGCAGAGTCGGGTGGTTCTGTGCGGGACCCCGTGGGGTCAGTGGTACCAGACCCTGGAGGA
GGTGTTTATTGAAGTTCAGGTGCCACCAGGCACGTGCACCCAGGATATCCAGTGCGGCCTGCAAAGCCAGCATGTGGCAC
TGGCGGTGGGCGGCCACGAGATCCTCAAGGGCAAACTCTTTGATCTACAATAGCTGATGAGGGAACATGGACTTTGGAGG
ATAGAAAAATGGTTCGTATTGTTCTTACCAAGGCAGAG

Alignment

ORF - retro_cjac_2093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 59.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAPFEERSGVVPCGTPWGQWYQTLEEVFIEVQVPPGTRAQDIQCGLQSRHVALAVGGREILKGKLFD-S
          MSAPFEE.S.VV.CGTPWGQWYQTLEEVFIEVQVPPGT..QDIQCGLQS.HVALAVGG.EILKGKLFD.S
Retrocopy MSAPFEEQSRVVLCGTPWGQWYQTLEEVFIEVQVPPGTCTQDIQCGLQSQHVALAVGGHEILKGKLFD<S

Parental  TIADEGTWTLEDRKMVRIVLTKTK
          TIADEGTWTLEDRKMVRIVLTK..
Retrocopy TIADEGTWTLEDRKMVRIVLTKAE

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	0.02 RPM	6.48 RPM
SRP051959_heart	0.02 RPM	5.21 RPM
SRP051959_kidney	0.00 RPM	7.83 RPM
SRP051959_liver	0.00 RPM	9.21 RPM
SRP051959_lung	0.03 RPM	6.77 RPM
SRP051959_lymph_node	0.00 RPM	7.90 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.14 RPM
SRP051959_spleen	0.02 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2093 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2093 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005270	1 retrocopy	retro_amel_535,
Bos taurus	ENSBTAG00000014772	1 retrocopy	retro_btau_1735,
Callithrix jacchus	ENSCJAG00000015367	1 retrocopy	retro_cjac_2093 ,
Cavia porcellus	ENSCPOG00000000877	1 retrocopy	retro_cpor_936,
Dipodomys ordii	ENSDORG00000014291	1 retrocopy	retro_dord_188,
Macropus eugenii	ENSMEUG00000004802	1 retrocopy	retro_meug_1673,
Myotis lucifugus	ENSMLUG00000001670	1 retrocopy	retro_mluc_1154,
Monodelphis domestica	ENSMODG00000007641	2 retrocopies	retro_mdom_1058, retro_mdom_2016,
Ornithorhynchus anatinus	ENSOANG00000021414	1 retrocopy	retro_oana_122,
Oryctolagus cuniculus	ENSOCUG00000005783	1 retrocopy	retro_ocun_819,
Otolemur garnettii	ENSOGAG00000024929	3 retrocopies	retro_ogar_1486, retro_ogar_1696, retro_ogar_482,
Sarcophilus harrisii	ENSSHAG00000007551	1 retrocopy	retro_shar_559,
Ictidomys tridecemlineatus	ENSSTOG00000028665	1 retrocopy	retro_itri_1770,
Tupaia belangeri	ENSTBEG00000000307	1 retrocopy	retro_tbel_507,
Tarsius syrichta	ENSTSYG00000008090	1 retrocopy	retro_tsyr_1638,