RetrogeneDB ID: retro_cjac_2958

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:150043297..150044897(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012324
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2958
ATGGCCTTTGCAAACCTGCGGAAAGTGCTCATCAGCGACAGCCTGGACCCTTGCTGCCGGAGGATCTTGCAAGATGGAGG
GCTGCAGGTGGTGGAGAAGCAGAACCTTAGCAAAGAAGAGCTGATAGCCAAGCTGCAGGACTGTGAAGGCCTCATCGTCC
GCTCTGCCACCAAGGTGACCGCTGATGTTATCAGTGCAGCTGAGAAGCTCCAGGTGGTGGGCAGGGCTGGCACAGGCGTG
GACAACGTGGACCTGGAAGCCGCCACAAAGAAGGGCGTCTTGGTCATGAACACCCCCAATGGGAACAGCCTCAGTGCTGC
AGAACTCACCTGCGGGATGATCCTGAGCCTGGCCAGGCAGATCCCCCAGGCGACGGCTTCGATGAAGGATGGCAAATGGG
AGCGGAAGAAGTTCATGGGAACAGAGCTGAATGGAAAGACCCTGGGAATTCTTGGCCTAGGCAGGATTGGGAGAGAGGTG
GCTACCCGGATGCAGTCCTTTGGGATGAAGACGATCGGGTATGACCCCATCATTTCCCCAGAGGTCTCGGCCTCCTTTGG
TGTTCAACAGCTGCCCCTGGAGGAGATCTGGCCTCTCTGTGATTTCATCACTGTGCACACTCCTCTCCTGCCCTCCACCA
CAGGCTTATTGAACGACGGCACCTTTGCCCAGTGCACGAAGGGGGTACGTGTGGTGAACTGCGCCCGTGGAGGGATCGTG
GACGAAAGACGCCCTGCTCCGGGCGCTGCAGTCTGGCCAGTGTGCCGGGGTTGCGCTGGACGTGTTTACGGAAGAGCCGC
CACGGGACCGAACCTTGGTGGATCATGAGAATGTCATCAGCTGTCCCCACCTGGGAGCCAGCACCAAGGAGGCGCAGAGC
CGTTGTGGGGAGGAAATTGCTGTTCAGTTCGTGGACATGGTGAAGGGGAAATCTCTCACGGGGGTTGTAAATGCCCAGGC
CCTTACCAGCGCCTTCTCTCCACACACCAAGCCTTGGATTGGTCTGGCAGAAGCTCTGGGGACACTGATGCGAGCTTGGG
CTGGGTCTCCCAAAGGGACCATCCAGGTGATAACACAAGGAGCGCCCCTGAAGAACGCCGGGACCTGCCTAAGCCCTGCA
GTCATCGTCGGCCTCTTGAAGGAGGCTTCCAAGCAGGCGGATGTGAACTTGGTGAACGCCAAGCTGCTGGTGGAAGAGGC
TGGCCTCAATGTCACCACCTCCCACAGCCTGGCAGCACCAGGGGAGCAGGGTTTCGGTGAATGTCTCCTGGCCGTGGCCC
TGGCAGGCACCCCTTACCAGGCTGTGGGCTTGGTCCAGGGCACCACACCTGTGCTGCAGGGGCTCAACCGAGCTGTCTTC
AGGCCAGAAGTGCCTCTCCGCAGGGGCCTGCCCCTGCTCCTATTCCGGACTCAGACCTCCGACCCTGCAATGCTGCCTAC
CATGATTGGCCTCCTGGCAGAGGCAGGCGTGCGGCTGCTGTCCTACCAGACTTCACTGGTGTCAGACGGGGAGACCTGGC
ACGTCATGGGCATCTCCTCCTTGCTGCCCAGCCTGGAAGCGTGGAAGCAGCATGTGACCGAGGCCTTCCAGTTCCACTTC

Alignment

ORF - retro_cjac_2958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFANLRKVLISDSLDPCCRRILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVISAAEKL
          MAFANLRKVLISDSLDPCCRRILQDGGLQVVEKQNLSKEELIA.LQDCEGLIVRSATKVTADVISAAEKL
Retrocopy MAFANLRKVLISDSLDPCCRRILQDGGLQVVEKQNLSKEELIAKLQDCEGLIVRSATKVTADVISAAEKL

Parental  QVVGRAGTGVDNVDLEAATRKGVLVMNTPNGNSLSAAELTCGMILSLARQIPQATASMKDGKWERKKFMG
          QVVGRAGTGVDNVDLEAAT.KGVLVMNTPNGNSLSAAELTCGMILSLARQIPQATASMKDGKWERKKFMG
Retrocopy QVVGRAGTGVDNVDLEAATKKGVLVMNTPNGNSLSAAELTCGMILSLARQIPQATASMKDGKWERKKFMG

Parental  TELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEISASFGVQQLPLEEIWPLCDFITVHTPLL
          TELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPE.SASFGVQQLPLEEIWPLCDFITVHTPLL
Retrocopy TELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTPLL

Parental  PSTTGLLNDGTFAQCKKGVRVVNCARGGIVDE-GALLRALQSGQCAGAALDVFTEEPPRDRTLVDHENVI
          PSTTGLLNDGTFAQC.KGVRVVNCARGGIVDE..ALLRALQSGQCAG.ALDVFTEEPPRDRTLVDHENVI
Retrocopy PSTTGLLNDGTFAQCTKGVRVVNCARGGIVDE>DALLRALQSGQCAGVALDVFTEEPPRDRTLVDHENVI

Parental  SCPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGS
          SCPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGS
Retrocopy SCPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGS

Parental  PKGTIQVITQGAPLKNAGTCLSPAVIVGLLKEASKQADVNLVNAKLLVEEAGLNVTTSHSLAAPGEQGFG
          PKGTIQVITQGAPLKNAGTCLSPAVIVGLLKEASKQADVNLVNAKLLVEEAGLNVTTSHSLAAPGEQGFG
Retrocopy PKGTIQVITQGAPLKNAGTCLSPAVIVGLLKEASKQADVNLVNAKLLVEEAGLNVTTSHSLAAPGEQGFG

Parental  ECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRGLPLLLFRTQTSDPAMLPTMIGLLAEAG
          ECLLAVALAG.PYQAVGLVQGTTPVLQGLN.AVFRPEVPLRRGLPLLLFRTQTSDPAMLPTMIGLLAEAG
Retrocopy ECLLAVALAGTPYQAVGLVQGTTPVLQGLNRAVFRPEVPLRRGLPLLLFRTQTSDPAMLPTMIGLLAEAG

Parental  VRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
          VRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
Retrocopy VRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF

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	0.80 RPM	16.00 RPM
SRP051959_heart	0.11 RPM	3.02 RPM
SRP051959_kidney	0.07 RPM	1.31 RPM
SRP051959_liver	0.15 RPM	2.66 RPM
SRP051959_lung	0.39 RPM	6.85 RPM
SRP051959_lymph_node	0.71 RPM	9.38 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.37 RPM
SRP051959_spleen	0.23 RPM	3.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2958 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2958 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,