RetrogeneDB ID: retro_cjac_1434

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:92112269..92113196(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMD14
• Ensembl ID: ENSCJAG00000005572
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 [Source:HGNC Symbol;Acc:16889]

Sequence

>retro_cjac_1434
ATGGACAGACTTCTGAGACTTGGAGGAGGTATGCCTGGACTGGGCCAGGGGCCACCTACAGAGGCTCCTGCAGTGGACAC
AGCAGAACAAGTCTATATCTCTTCCCTGGCACTGTTAAAAATGTTAAAACATGGTCGTGCTGGAGTTCCAATGGAAGTTA
TGGGTTTGATGCTTGGAGAATTTGTTGATGATTATACCGTCAGAGTGATTGATGTGTTTGCTATTCCACAATCAGGAACA
GGTGTCAGTGTAGAGGCACTTGATCCAGTGTTCCAAGCCAAAATGTTGGATATGTTGAAGCAGACAGGAAGGCCGGAGAT
GGTTGTTGGTTGGTATCACAGTCACCCTGGCTTTGGTTGTTGGCTTTCTGGTGTGGATATCAACACTCAGCAGAGCTTTG
AAGCTTTGTTGGAGAGAGCTGTGGCAGTGGTTGTGGATCCCATTCAGAGTGTAAAAGGAAAGGTTGTTATTGATGCCTTC
AGATTGATCAATGCTAATATGATGGTCTTAGGACATGAACCAAGACAAACAACTTCAAATCTGGGTCACTTAAACAAGCC
ATCTGCCCAGGCATTAATTCATGGACTAAACAGACATTATTACTCCATTACCATTAACTATCGGGAAAATGAACTGGAAC
AGAAGATGCTGCTAAATTTGCATAAGAGGAGTTGGATGGAAAGTTTGACACTTCAGGACTACAGTGAACATTGTAAACAT
AATGAATCAGTGGTAAAAGAGATGTTGGAATTAGCCAAGAATTACAATAAGGCTGTAGAAGAAGATAAGATGACACCTGA
ACAGCTGGCAATAAAGAATGTTGGCAAGCAGGACCCCAAACGTCATTTGGAGGAACATGTGGATGTACTTATGACTTCAA
ATATTGTCCAGTGTTTAGCAGCTATGTTGGATACTGTTGTATTTAAA

Alignment

ORF - retro_cjac_1434 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVRVI
          MDRLLRLGGGMPGLGQGPPT.APAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVRVI
Retrocopy MDRLLRLGGGMPGLGQGPPTEAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVRVI

Parental  DVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERA
          DVFA.PQSGTGVSVEA.DPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEAL.ERA
Retrocopy DVFAIPQSGTGVSVEALDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALLERA

Parental  VAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGLNRHYYSITINYRKN
          VAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPS.QALIHGLNRHYYSITINYR.N
Retrocopy VAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSAQALIHGLNRHYYSITINYREN

Parental  ELEQKMLLNLHKKSWMEGLTLQDYSEHCKHNESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDP
          ELEQKMLLNLHK.SWME.LTLQDYSEHCKHNESVVKEMLELAKNYNKAV.EEDKMTPEQLAIKNVGKQDP
Retrocopy ELEQKMLLNLHKRSWMESLTLQDYSEHCKHNESVVKEMLELAKNYNKAV-EEDKMTPEQLAIKNVGKQDP

Parental  KRHLEEHVDVLMTSNIVQCLAAMLDTVVFK
          KRHLEEHVDVLMTSNIVQCLAAMLDTVVFK
Retrocopy KRHLEEHVDVLMTSNIVQCLAAMLDTVVFK

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	0.07 RPM	24.18 RPM
SRP051959_heart	0.07 RPM	18.47 RPM
SRP051959_kidney	0.07 RPM	22.79 RPM
SRP051959_liver	0.02 RPM	16.92 RPM
SRP051959_lung	0.00 RPM	14.71 RPM
SRP051959_lymph_node	0.00 RPM	16.57 RPM
SRP051959_skeletal_muscle	0.13 RPM	34.94 RPM
SRP051959_spleen	0.06 RPM	19.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1434 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1434 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002556	1 retrocopy	retro_chof_2387,
Callithrix jacchus	ENSCJAG00000005572	1 retrocopy	retro_cjac_1434 ,
Gorilla gorilla	ENSGGOG00000015747	1 retrocopy	retro_ggor_1710,
Mus musculus	ENSMUSG00000026914	1 retrocopy	retro_mmus_701,
Otolemur garnettii	ENSOGAG00000004933	2 retrocopies	retro_ogar_2955, retro_ogar_3213,
Pongo abelii	ENSPPYG00000012881	1 retrocopy	retro_pabe_2100,
Pan troglodytes	ENSPTRG00000012575	1 retrocopy	retro_ptro_1636,
Rattus norvegicus	ENSRNOG00000004911	1 retrocopy	retro_rnor_1271,
Tupaia belangeri	ENSTBEG00000014118	1 retrocopy	retro_tbel_3917,