RetrogeneDB ID: retro_cjac_3994

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286730.1:112..1303(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022804
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3994
CAGTTCATGGGAACAGAGCTGAATGGAAAGATCCTGGGAATTTTGGGCCTGGGAGGGATTGGGAGGAAGGTGGCTACCCG
GATGCAGTCCTTTGGGATGAAGATGATAGGGTATGACCCCATCATTTCCTCAGAGGTCTTGGCCTCCTTTGGTGTTCAGT
AACTGCCCCTGGAGGAGATCTGGCCTCTCTGTGATTTCATCACTGTGCACACTCCTCTCCTGCCCTCCACCAAAGGCTTA
TTGAACAATAGCACCTTTGTCCAGTACAAGAAGGGGGTACGTGTGGTGAACTGTGCCCGCGGAGGGATCGTGGACGATGG
CGCCCTTCTCTGGGCCCTGCAGTCTGGCCAGTATGCTGGGGCTGCGCTGGACATGTTTACGGAAGAGCCACCACAGGATC
GAAACTTGGTGGACCATGAGAATGTCATCAGCTGTCCCCACCTGGGCGCCAGCACCAAGGAGGCACAGAGCTGCCGTGGG
GAGGAAATTGCTGTTCCGTTCGTGGACATGGTGAAGGGGAAATCTCTCACAGGGGTTGTAAATGCCCAGGCCCTTACCAG
CGCCTTCTCTCCACACACCAAGCCTTGGATCGGTCTGGCAGAAGCTCTGGGGACACTGATGCAAGCCTGGGCTGGGTCTC
CCAAAGGGATCATCCAGGTGATTACACCAGGAACATCCCTGAAGAATGCTGGGAACTGCCTAAGCCCTGCAGTCATCATC
GGCTTCTTGAAGGAGGCTTCCAAGCAGGCGGATGTGAACTTGGTGAATGCCAAGCTGCTGGTGAAAGAGGCTGGCCTCAG
TGTCACCACCTCCCACAGCCCAGCAGCACCAGGGGAGCAGGGCTTCGGGGAATGTCTCCTGGCCGTGGCCCTGGCAGGCA
CCCCTTACCAGGCTGCGGGTTTGGTCCAGGGCACCACACCTGTGCTGCAAGGGCTCAATGGAGCTGTCTTCAGGCCAGAA
GTGCCTCTCTGCAGGGGCCTGCCCCTGCTCCTATTCTGGACTCAGGCTTCTGACCCTGCAATGCTGCCTACCATGATTGG
CCTCCTGGCAGAGGCAGGCATGCGGCTGCTTTCCTATCAGACTTTACTGGTGTCAGATGGGGAGACCTGGCACATCATGG
GCATCTCCTCCTTGCTGCCCAGCCTGGAAGCATGGAAGCAGCATGTGACTGAGGCCTTCCAGTTTCACTTC

Alignment

ORF - retro_cjac_3994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.42 %
• Parental protein coverage: 74.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KFMGTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEISASFGVQQLPLEEIWPLCDFITVH
          .FMGTELNGK.LGILGLG.IGR.VATRMQSFGMK.IGYDPIIS.E..ASFGVQ.LPLEEIWPLCDFITVH
Retrocopy QFMGTELNGKILGILGLGGIGRKVATRMQSFGMKMIGYDPIISSEVLASFGVQ*LPLEEIWPLCDFITVH

Parental  TPLLPSTTGLLNDGTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRTLVDHE
          TPLLPST.GLLN..TF.Q.KKGVRVVNCARGGIVD.GALL.ALQSGQ.AGAALD.FTEEPP.DR.LVDHE
Retrocopy TPLLPSTKGLLNNSTFVQYKKGVRVVNCARGGIVDDGALLWALQSGQYAGAALDMFTEEPPQDRNLVDHE

Parental  NVISCPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAW
          NVISCPHLGASTKEAQS..GEEIAV.FVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLM.AW
Retrocopy NVISCPHLGASTKEAQSCRGEEIAVPFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMQAW

Parental  AGSPKGTIQVITQGAPLKNAGTCLSPAVIVGLLKEASKQADVNLVNAKLLVEEAGLNVTTSHSLAAPGEQ
          AGSPKG.IQVIT.G..LKNAG.CLSPAVI.G.LKEASKQADVNLVNAKLLV.EAGL.VTTSHS.AAPGEQ
Retrocopy AGSPKGIIQVITPGTSLKNAGNCLSPAVIIGFLKEASKQADVNLVNAKLLVKEAGLSVTTSHSPAAPGEQ

Parental  GFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRGLPLLLFRTQTSDPAMLPTMIGLLA
          GFGECLLAVALAG.PYQA.GLVQGTTPVLQGLNGAVFRPEVPL.RGLPLLLF.TQ.SDPAMLPTMIGLLA
Retrocopy GFGECLLAVALAGTPYQAAGLVQGTTPVLQGLNGAVFRPEVPLCRGLPLLLFWTQASDPAMLPTMIGLLA

Parental  EAGVRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
          EAG.RLLSYQT.LVSDGETWH.MGISSLLPSLEAWKQHVTEAFQFHF
Retrocopy EAGMRLLSYQTLLVSDGETWHIMGISSLLPSLEAWKQHVTEAFQFHF

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3994 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3994 has 0 orthologous retrocopies within eutheria group .

---

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,