RetrogeneDB ID: retro_cjac_3441

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01179703.1:5625..6626(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000014228
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHGDH
• Ensembl ID: ENSCJAG00000019916
• Aliases: None
• Description: None

Sequence

>retro_cjac_3441
TGTGATTTCATCACTGTGCAGACTCCTCTCCTGCCCTCCACCACAGGCTTATTGAACAACAGCACCTTTGTCCAGTGCAA
GAAGTGGGTAAGTGTGGTGAACTGCGCCCGCGGAGGGATCGTGGACGATGGCTCCCTGCTCCCGGCCCTGCAGTCGGGCC
AGTGTTCCGGGGCTGCGCTGGACGTGTTTACGGAAGAGCCACCATGGGACCGAACCTTGGTGGACCATGAGAATGTCATC
AGCTGTCCCCACCTGGGCGCCGCACCAAGGAGGTGCAGAGCCGCTGTGGGGAGGAAATTTTTGTTCGGTTTGTGGACATG
GTGAAGGGGAAATCTCTCACAGGGGTTGTAAATGCCCAGGCCCCTACCAGCGCCTTCTCTCCACACATCAAGCCTTGGAT
TGGTCTGGCAGAAGCTCTGGGGACACTGGTGCGAGCCTGGGCTGGGTCTCCCAAAGGGACCATCCAGGTGATAACACCAG
GAACATCCCTGAAGAATGCTGGGAACTGCCTAAGCCCTGCAGTCATCGTCGGCCTCTTGAAGGAGGCTTCCAAGCAGACG
GATGTAAACTTGGTGAACGCCAAGCTGCTGGTGAAAGAGGCTGGCCTCAGTGTCACCACCTCCCACAGCCCGGCAGCACC
AGGGGAGCAGGGCTTCGGGGAATGTCTCCTGGCCATGGCCCTATCAGGCGCCCCTTACCAGGCTGCGGGTTTGGTCCAGG
GCACCACACCTATGCTGCAGGGGCTCAATGGAGCCGTCTTCAGGCCGGAAGTGCCTCTCTGCAGGGGCCTGCTTCTGCTC
CTATTCAAGACTCAGGCTTCCGACACTGCAATGCTGCCTATCACGATTGGCCTCCTGGCAGAGGCAGGCGTGCGGCTGCT
TTCCTACCAGACTTCACTGGTGTCAGACGGGGAGACCTGGCACATCATGAGCAACTCCTCCTTGCTGCCCAGCCTGGAAG
CATGGAAGCAGCATGTGACCGAGGCCTTCCAGTTCCACTTC

Alignment

ORF - retro_cjac_3441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 62.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CDFITVHTPLLPSTTGLLNDGTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRD
          CDFITV.TPLLPSTTGLLN..TF.QCKK.V.VVNCARGGIVD.G.LL.ALQSGQC.GAALDVFTEEPP.D
Retrocopy CDFITVQTPLLPSTTGLLNNSTFVQCKKWVSVVNCARGGIVDDGSLLPALQSGQCSGAALDVFTEEPPWD

Parental  RTLVDHENVISCPHLGAS-TKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEA
          RTLVDHENVISCPHLGA..TKE.QSRCGEEI.V.FVDMVKGKSLTGVVNAQA.TSAFSPH.KPWIGLAEA
Retrocopy RTLVDHENVISCPHLGAA<TKEVQSRCGEEIFVRFVDMVKGKSLTGVVNAQAPTSAFSPHIKPWIGLAEA

Parental  LGTLMRAWAGSPKGTIQVITQGAPLKNAGTCLSPAVIVGLLKEASKQADVNLVNAKLLVEEAGLNVTTSH
          LGTL.RAWAGSPKGTIQVIT.G..LKNAG.CLSPAVIVGLLKEASKQ.DVNLVNAKLLV.EAGL.VTTSH
Retrocopy LGTLVRAWAGSPKGTIQVITPGTSLKNAGNCLSPAVIVGLLKEASKQTDVNLVNAKLLVKEAGLSVTTSH

Parental  SLAAPGEQGFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRGLPLLLFRTQTSDPAML
          S.AAPGEQGFGECLLA.AL.GAPYQA.GLVQGTTP.LQGLNGAVFRPEVPL.RGL.LLLF.TQ.SD.AML
Retrocopy SPAAPGEQGFGECLLAMALSGAPYQAAGLVQGTTPMLQGLNGAVFRPEVPLCRGLLLLLFKTQASDTAML

Parental  PTMIGLLAEAGVRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
          P..IGLLAEAGVRLLSYQTSLVSDGETWH.M..SSLLPSLEAWKQHVTEAFQFHF
Retrocopy PITIGLLAEAGVRLLSYQTSLVSDGETWHIMSNSSLLPSLEAWKQHVTEAFQFHF

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	0.09 RPM	16.00 RPM
SRP051959_heart	0.04 RPM	3.02 RPM
SRP051959_kidney	0.04 RPM	1.31 RPM
SRP051959_liver	0.00 RPM	2.66 RPM
SRP051959_lung	0.07 RPM	6.85 RPM
SRP051959_lymph_node	0.00 RPM	9.38 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.37 RPM
SRP051959_spleen	0.02 RPM	3.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3441 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3441 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012539	2 retrocopies	retro_cjac_1866, retro_cjac_2528,
Callithrix jacchus	ENSCJAG00000019916	4 retrocopies	retro_cjac_2894, retro_cjac_2958, retro_cjac_3441 , retro_cjac_3994,
Myotis lucifugus	ENSMLUG00000002986	1 retrocopy	retro_mluc_2502,
Mus musculus	ENSMUSG00000053398	16 retrocopies	retro_mmus_1008, retro_mmus_1223, retro_mmus_1384, retro_mmus_1708, retro_mmus_1835, retro_mmus_1892, retro_mmus_2057, retro_mmus_2169, retro_mmus_2889, retro_mmus_2979, retro_mmus_3021, retro_mmus_3176, retro_mmus_3180, retro_mmus_3217, retro_mmus_3441, retro_mmus_545,
Rattus norvegicus	ENSRNOG00000019328	1 retrocopy	retro_rnor_452,