RetrogeneDB ID: retro_cjac_4070

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:58171924..58172647(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032661
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK14
• Ensembl ID: ENSCJAG00000014175
• Aliases: None
• Description: Cyclin-dependent kinase 14 [Source:UniProtKB/Swiss-Prot;Acc:B0VXE8]

Sequence

>retro_cjac_4070
ATGTGCGACCTCATTGAGCCGCAGCTGGCTGAGAAGATCAGCAAGATGAAGAAGTTGTGGAGAACTTTGTCAGAGAGTTT
CAGCCATATTGCTTTGAAGAAAGATGACACCACCTTTGATGAGATATGTGTCACAAAGATGTCTAAACGGAATTGCCAGG
GAATGGACTCAGTGATCAAACCCCTGGACACAATTCCTGAGGACAAAAAAGTCAGAGTTCAGAGGACACAGAGCACTTTT
GACCCATTTGAGAAACCAACTAATCAAGTAAAGAAGGTGCATTCTGAGAACAATGCTTGCATTAACTTTAAGACCTCCTC
CACTGGCAAAGAGTCACCTAAAATTAGGCGGCACTCCAGCCCCAGTTCGCCAACAAGTCCCAAATTTGGAAAAGCTGACC
CATACGAAAAACTGGAAAAACTAGGGGAAGAATCTTACGCTACAGTATATGAAGGGAAAAGCAAGGTAAATGGAAAGTTG
GTAGCTCTGAAGGTGATCAGGCTGCAAGAAGAAGAAGGGACACCTTTCACAGCTATCAGGGAAGCTTCTCTGTTAAAAGG
ACTAAAACACACTAACATAGTGCAACTTCATGACATCATACATACCAAGGAGATGCTGACACTTGTGTTTGAATATGTGC
ACACTGATTTATGTCAGTACATGGACAAGCACCCTGGCGGACTGCATCCAGATAATGTGAAGTTGTTTTTATTTCAGTTG
CTG

Alignment

ORF - retro_cjac_4070 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.61 %
• Parental protein coverage: 51.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDLIEPQPAEKIGKMKKLRRTLSESFSRIALKKDDTTFDEICVTKMSTRNCQGMDSVIKPLDTIPEDKK
          MCDLIEPQ.AEKI.KMKKL.RTLSESFS.IALKKDDTTFDEICVTKMS.RNCQGMDSVIKPLDTIPEDKK
Retrocopy MCDLIEPQLAEKISKMKKLWRTLSESFSHIALKKDDTTFDEICVTKMSKRNCQGMDSVIKPLDTIPEDKK

Parental  VRVQRTQSTFDPFEKPTNQVKRVHSENNACINFKTSSTGKESPKVRRHSSPSSPTSPKFGKADSYEKLEK
          VRVQRTQSTFDPFEKPTNQVK.VHSENNACINFKTSSTGKESPK.RRHSSPSSPTSPKFGKAD.YEKLEK
Retrocopy VRVQRTQSTFDPFEKPTNQVKKVHSENNACINFKTSSTGKESPKIRRHSSPSSPTSPKFGKADPYEKLEK

Parental  LGEGSYATVYKGKSKVNGKLVALKVIRLQEEEGTPFTAIREASLLKGLKHANIVLLHDIIHTKETLTLVF
          LGE.SYATVY.GKSKVNGKLVALKVIRLQEEEGTPFTAIREASLLKGLKH.NIV.LHDIIHTKE.LTLVF
Retrocopy LGEESYATVYEGKSKVNGKLVALKVIRLQEEEGTPFTAIREASLLKGLKHTNIVQLHDIIHTKEMLTLVF

Parental  EYVHTDLCQYMDKHPGGLHPDNVKLFLFQLL
          EYVHTDLCQYMDKHPGGLHPDNVKLFLFQLL
Retrocopy EYVHTDLCQYMDKHPGGLHPDNVKLFLFQLL

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	3.99 RPM
SRP051959_heart	0.00 RPM	12.05 RPM
SRP051959_kidney	0.00 RPM	17.31 RPM
SRP051959_liver	0.00 RPM	12.61 RPM
SRP051959_lung	0.00 RPM	17.63 RPM
SRP051959_lymph_node	0.00 RPM	3.54 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.72 RPM
SRP051959_spleen	0.02 RPM	11.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4070 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4070 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4070 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012973	1 retrocopy	retro_chof_2240,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Callithrix jacchus	ENSCJAG00000012261	1 retrocopy	retro_cjac_961,
Callithrix jacchus	ENSCJAG00000014175	1 retrocopy	retro_cjac_4070 ,
Callithrix jacchus	ENSCJAG00000020258	1 retrocopy	retro_cjac_1522,