RetrogeneDB ID: retro_cjac_2281

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:137953431..137954826(-)
• Located in intron of: ENSCJAG00000018237

Retrocopy information

• Ensembl ID: ENSCJAG00000021900
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CPNE9
• Ensembl ID: ENSCJAG00000016038
• Aliases: CPNE9, copine-9
• Description: None

Sequence

>retro_cjac_2281
TACAACGTGGACTCCAAAACCAACATCTCCAAACCGGATTTCCTGGGACAAGCGTTCCTGGCCCTGGGAGAGGTGATTGG
AGGCCAGGGCAGCCACATAGAGCGAACCCTCACGGGTGTAGCAGGCAAGAAGTGTGGGACCATATTGCTGACTGCAGAAG
AGCTTAGCAATTGTCAGGACATTGCCACCATGCTGCTGTGTGCCAACAAGCTGGACAAGAAGGACTTCTTTGGGAAATCA
GACCCCTTCCTTGTGTTCTACAGGAGCAATGAAGATAGCACATTCACCATCTGCCACAAGACAGAGGTTGTGAAAAACAC
ACTGAATCCTGTGTGGCAGCCCTTCAGCATCCCTGTGCGGGCTCTGTACAATGGAGACTATGACAGAACAGTGAAGACTG
ATGTGTACGACTGGGACCGGAATGGAAGCCACGATTTCACTGGGGAGTTCACCACCAGCTACCGGGAGCTCAGCAAGGCC
CAGAACCAGTTCACAGTAAATGAGGTACTTAACCCTCGGAAGAAATGTAAGAAGAAGAAATATGTCAACTCGGGAACTGT
GACGCTGCTCTCCTTCTCTGTGGACTCTGAATTCACTTTTGTTGATTACATCAAGGGAGGGACACAGCTGAACTTCACAG
TAGCTATTGACTTTACAGCTTCCAATGGGAATCCTCTGCAATCTATCTCCCTGCACTACATGAGTCCCTACCAGCTCAGC
GCCTATGCCATGGCCCTCAAGGCAGTGGGAGAGATCATCCAGGACTATGACAGTGACAAGCTCTTCCCAGCTTATGGCTT
TGGAGCCAAGCTGCCCCCAGAGGGACGGATCTCCCACCAGTTCCCCCTGAACAACAATGATGAGGACCCCAACTGTGCGG
GCATTGAGGGTGTGTTGGAGAGCTATTTCCAGAGCCTGCACACAGTGCAGCTCTATGGGCCCACCTACTTTGCTCCTGTC
ATCAACCAAGTGGCCAGGGCTGCAGCCAAGATCTCTGATGGTTCCCAGTACTATGTTCTGCTCATCATCGCTGATGGAGT
CATCTCTGACATGACGCAGACCAAGGAGGCCATCGTCAGCACCTCCTCACTGCCCATGTCTATCATTATCGTCGGTGTAG
GACCAGCCAAGTTTGAGGCAATGGAAGAGTTGGATGGTGATGATATGCGTGTGTCCTCTGGGGGATGCTACGCAGAGCGG
GACATCGTTCAGTTCGTCCCATTCCGAGACTATGTGGACCAGTTGGGGAACCAGGTGTTGAGCATGGCCCGACTGACCAA
GGATGAGCTGGCTGAGATCCCGGAGCAGTTGCTGTCCTGTATGCGTACCAGAGACATCCAGCCTCGGCCCCCACCCCCTG
TCAACCCCAGCCCGACTCCAGCTCCAGAGCAGCCC

Alignment

ORF - retro_cjac_2281 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.42 %
• Parental protein coverage: 84.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YNVDSKTNISKPKDFLGQAFLALGEVIGGQGSRVERTLTGVPGKKCGTILLTAEELSNCRDIATMQLCAN
          YNVDSKTNISKP.DFLGQAFLALGEVIGGQGS..ERTLTGV.GKKCGTILLTAEELSNC.DIATM.LCAN
Retrocopy YNVDSKTNISKP-DFLGQAFLALGEVIGGQGSHIERTLTGVAGKKCGTILLTAEELSNCQDIATMLLCAN

Parental  KLDKKDFFGKSDPFLVFYRSNEDGTFTICHKTEVVKNTLNPVWQPFSIPVRALCNGDYDRTVKIDVYDWD
          KLDKKDFFGKSDPFLVFYRSNED.TFTICHKTEVVKNTLNPVWQPFSIPVRAL.NGDYDRTVK.DVYDWD
Retrocopy KLDKKDFFGKSDPFLVFYRSNEDSTFTICHKTEVVKNTLNPVWQPFSIPVRALYNGDYDRTVKTDVYDWD

Parental  RDGSHDFIGEFTTSYRELSKAQNQFTVYEVLNPRKKCKKKKYVNSGTVTLLSFSVDSEFTFVDYIKGGTQ
          R.GSHDF.GEFTTSYRELSKAQNQFTV.EVLNPRKKCKKKKYVNSGTVTLLSFSVDSEFTFVDYIKGGTQ
Retrocopy RNGSHDFTGEFTTSYRELSKAQNQFTVNEVLNPRKKCKKKKYVNSGTVTLLSFSVDSEFTFVDYIKGGTQ

Parental  LNFTVAIDFTASNGNPLQPTSLHYMSPYQLSAYAMALKAVGEIIQDYDSDKLFPAYGFGAKLPPEGRISH
          LNFTVAIDFTASNGNPLQ..SLHYMSPYQLSAYAMALKAVGEIIQDYDSDKLFPAYGFGAKLPPEGRISH
Retrocopy LNFTVAIDFTASNGNPLQSISLHYMSPYQLSAYAMALKAVGEIIQDYDSDKLFPAYGFGAKLPPEGRISH

Parental  QFPLNNNDEDPNCAGIEGVLESYFQSLRTVQLYGPTYFAPVINQVARAAAKISDGSQYYVLLIITDGVIS
          QFPLNNNDEDPNCAGIEGVLESYFQSL.TVQLYGPTYFAPVINQVARAAAKISDGSQYYVLLII.DGVIS
Retrocopy QFPLNNNDEDPNCAGIEGVLESYFQSLHTVQLYGPTYFAPVINQVARAAAKISDGSQYYVLLIIADGVIS

Parental  DMTQTKEAIVSASSLPMSIIIVGVGPAMFEAMEELDGDDVRVSSRGRYAERDIVQFVPFRDYVDRSGNQV
          DMTQTKEAIVS.SSLPMSIIIVGVGPA.FEAMEELDGDD.RVSS.G.YAERDIVQFVPFRDYVD..GNQV
Retrocopy DMTQTKEAIVSTSSLPMSIIIVGVGPAKFEAMEELDGDDMRVSSGGCYAERDIVQFVPFRDYVDQLGNQV

Parental  LSMARLAKDVLAEIPEQLLSYMRTRDIQPRPPPPVNPSPTPAPEQP
          LSMARL.KD.LAEIPEQLLS.MRTRDIQPRPPPPVNPSPTPAPEQP
Retrocopy LSMARLTKDELAEIPEQLLSCMRTRDIQPRPPPPVNPSPTPAPEQP

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	0.00 RPM	0.11 RPM
SRP051959_heart	0.00 RPM	0.25 RPM
SRP051959_kidney	0.02 RPM	0.11 RPM
SRP051959_liver	0.00 RPM	0.09 RPM
SRP051959_lung	0.00 RPM	0.24 RPM
SRP051959_lymph_node	0.00 RPM	0.43 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.07 RPM
SRP051959_spleen	0.00 RPM	0.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2281 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2281 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016038	1 retrocopy	retro_cjac_2281 ,