RetrogeneDB ID: retro_cjac_3230

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:76067838..76068780(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022273
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CPPED1
• Ensembl ID: ENSCJAG00000016005
• Aliases: None
• Description: calcineurin-like phosphoesterase domain containing 1 [Source:HGNC Symbol;Acc:25632]

Sequence

>retro_cjac_3230
ATGTCGACTGCAGAGGCGGCGGGTGTTTTCCATAAAGCCCGGAACAGGACCCTGGACGCGTTTCCCGCAGAAAAGGAAGG
GGAATGGAAAGGCCCATTCTACTTCATCCTGGGCACAGACCCACAGTTTGGGTTGATGAAGGCCTGGTCCACTGGGGACT
GTGACAATGGTGGTGACGAATGGGGACAGGAGATCCGTCTAACTGAGCAAGCTGTCCAGGCTGTCAACAAGCTGAACCCC
AAACCCAAATTCTTTGTTCTGTGCGGCGACCTCATCCACGCCATGCCCGGGAAGCCGTGGCGGAAGGAGCAGACAGAGGA
CCTGCAGCGAGTGCTCAAGACAGTGGACAGGGCCATCCCACTGGTCCTTGTCAGCGGCAACCACGACATTGGCAATGTCC
CCACATCCGAGACCATTGAGGAGTTCTGCCAGACTTGGGGAGATGACTACTTTAGCTTCTGGGTCGGAGGTGTGCTGTTC
CTGGTCCTCAACTCCCAGTTCTACGAGAACCCCTCCAAATGTCCTGGCCTGAAGCAGGCACAGGACCAGTGGCTGGATGA
GCAGCTGAACATCGCGAGGCAGCGGAACTGCCAGCATGCCATCGTCTTCCAGCACATCCCACTGTTCCTGAAAAGCATCG
ATGAGGATGACGACGACTACTTCAACCTCAGCAAGCCCGCTCGGAAGAGGTTGGCAGACAAGTTCATCCACGCAGGTGTC
AAAGCCGTGTTCTCAGGCCACTACCACAGGAATGCTGGGGGCACCTACCAGAACCTCGACATGGTGGTGTCATCCGCCAT
CGGATGCCAGCTGGGCCTAGACCCCCACGGGCTCCGAGTTGTGGTGGTCACTGCTGACAAAATTGTTCACCGATACTACA
GTCTGGATGAGCTGAGTGAGAAAGGAATAGAAGACGATCTCATGGATTTGATAAAGAAAAAA

Alignment

ORF - retro_cjac_3230 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTAEAGGVFHKARNRTLDAFPAEKEGEWKGPFYFILGTDPQFGLMKAWSTGDCDNGGDEWGQEIRLTEQ
          MSTAEA.GVFHKARNRTLDAFPAEKEGEWKGPFYFILGTDPQFGLMKAWSTGDCDNGGDEWGQEIRLTEQ
Retrocopy MSTAEAAGVFHKARNRTLDAFPAEKEGEWKGPFYFILGTDPQFGLMKAWSTGDCDNGGDEWGQEIRLTEQ

Parental  AVQAINKLNPKPKFFVLCGDLIHAMPGKPWRKEQTEDLQRVLKTVDRAIPLVLVSGNHDIGNVPTSETIE
          AVQA.NKLNPKPKFFVLCGDLIHAMPGKPWRKEQTEDLQRVLKTVDRAIPLVLVSGNHDIGNVPTSETIE
Retrocopy AVQAVNKLNPKPKFFVLCGDLIHAMPGKPWRKEQTEDLQRVLKTVDRAIPLVLVSGNHDIGNVPTSETIE

Parental  EFCQTWGDDYFSFWVGGVLFLVLNSQFYENPSKCPGLKQAQDQWLDEQLNIARQRNCQHAIVFQHIPLFL
          EFCQTWGDDYFSFWVGGVLFLVLNSQFYENPSKCPGLKQAQDQWLDEQLNIARQRNCQHAIVFQHIPLFL
Retrocopy EFCQTWGDDYFSFWVGGVLFLVLNSQFYENPSKCPGLKQAQDQWLDEQLNIARQRNCQHAIVFQHIPLFL

Parental  KSIDEDDDDYFNLSKPARKRLADKFIHAGVKAVFSGHYHRNAGGTYQNLDMVVSSAIGCQLGLDPHGLRV
          KSIDEDDDDYFNLSKPARKRLADKFIHAGVKAVFSGHYHRNAGGTYQNLDMVVSSAIGCQLGLDPHGLRV
Retrocopy KSIDEDDDDYFNLSKPARKRLADKFIHAGVKAVFSGHYHRNAGGTYQNLDMVVSSAIGCQLGLDPHGLRV

Parental  VVVTADKIVHRYYSLDELSEKGIEDDLMDLIKKK
          VVVTADKIVHRYYSLDELSEKGIEDDLMDLIKKK
Retrocopy VVVTADKIVHRYYSLDELSEKGIEDDLMDLIKKK

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	6.68 RPM
SRP051959_heart	0.02 RPM	5.60 RPM
SRP051959_kidney	0.07 RPM	8.50 RPM
SRP051959_liver	0.13 RPM	13.52 RPM
SRP051959_lung	0.02 RPM	4.90 RPM
SRP051959_lymph_node	0.02 RPM	4.18 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.11 RPM
SRP051959_spleen	0.00 RPM	5.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3230 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3230 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	ENSCJAG00000016005	1 retrocopy	retro_cjac_3230 ,