RetrogeneDB ID: retro_mmus_3021

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:41666519..41668099(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091401
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Phgdh
• Ensembl ID: ENSMUSG00000053398
• Aliases: Phgdh, 3-PGDH, 3PGDH, 4930479N23, A10, PGAD, PGD, PGDH, SERA
• Description: 3-phosphoglycerate dehydrogenase [Source:MGI Symbol;Acc:MGI:1355330]

Sequence

>retro_mmus_3021
AAAATACTCATCAGTGACAGCCTGGACCCCTGCTGCCAGAAGATCCTACAAGATGGAGGGCTGCAGGTGGTGGAGAAGCA
GAACTTGAGCAAGGAGGAGCTGATAGCTGAACTCCAGGACTGTGAAGGCCTCATTGTCCGGTCAGCTACTAAGGTCATTG
CTGATGTCATTAATGCAGCAGAGAAGCTCCAGGTGGTGAGCAGGGCTGGCACAGGCGTGGACAATGTGGATCTGGAGGCT
GCCACGAGGAAGGGCATCCTACCCATGAACACCCCAACGGGAACAGCCTCAGTGCTGCGGAGCTCACCTGTGGAATGATC
ATGTGCCTGGCCAGACAGATTCCCCAGGCAACAGCTTCGATGAAAGATGGCAAATGGGACCAGAAGAAGTTCATGGGGAC
AGAACTGAACGGGAAGACACTGGGAATTCTTGGCCTCAGCAGAATCAGAAGAGAGGTGGCCACCCGAATGCAGTCCTTTG
GAATGAAGACTGTAGGCTATGATCCCATCATCTCTCCTGAAGTCGCGGCCTCCTTTGATGTTCAGTAGCTGCCGCTGGAG
GAGATCTGGCCTCTCTGTGACTTCATAACTGTCCATACCCCACTCCTGCCCTCCACCACAGGCTTGCTGAATGACAGCAC
CTTTGCTCAGTGCAAGAAAGGCATGCGCGTGGTGAACTGTGCTCGAGGAGGTACTGTGGATGAAGGTGCCCTGCTGCGTG
CCCTGCAGTCTGGTCAGTGTGCTGGGGCTGCACTGGATGTGTTTACAGAAGAGCCACCACAGGACCGGGCCTTAGTGGAA
CATGAGAAAGTCATCAGCTGTCCCCACCTGGGTGCCAGCACCAAGGAAGCCCAGAGCCACTGTGGGGAGGAAATCGCAGT
CCAGTTTGTAGACATGGTGAAGGAGAAATCTCTAACAAGCACCGTGAACGCCCAGGCCCTCACCAGTGCCTTCTCTCCAC
ACACCAAGCCTTGGATTGATCTGGCAGAAGCATTGGGCATGCTGATGCACGCCTGGGCTGGCTCCCCTAAAGGGACCATC
CAGGTGGTTACTCAAGGAACATCTCTGAAGAATGCTTGGGACCTGCCTGAGCCCTGCAGTCATTGTCGGCCTTCTGAGAG
AAGCATCTAAGCAGGCAGACGTGAACTTGGTGAACGCTAAGCTACTGGTGAAAGAGGCTGGCCTCAATGTCACCACCTCC
CACAACCCTGGGGCTCCAGGGGAGCAGGGCAGCGGGGAATGCCTCCTGACTGTGGCCCTGGCAGGTGACCCCTACCAAGT
TGTGTGGGCTTGATCCAGGGCACCACACTAATGCTGCAGATGCTCAACGGAGCTGTCTTCAGACGAGAGGTGCCACTACG
CAGGGGCCAACCCCTGCTCAAATTCCGGGCTCAGCCCTCCAACCCTGTGATGCTGCCCACTATGATCGGCCTCCTGGCAG
AGGCGGGTGTACAGCTACTGTCCTACCAAACCTCCATGGTGTCTGACGGAGAGCCCTAGTACGTCACGGGCCTCTCCTCC
CTACTGCCCAGCCTGGAAACATGGAAGTAGCATGTATTGGAGGTTTTCCAGTTCTGCTTC

Alignment

ORF - retro_mmus_3021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAG
          K.LISDSLDPCC.KILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKV.ADVINAAEKLQVV.RAG
Retrocopy KILISDSLDPCCQKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVIADVINAAEKLQVVSRAG

Parental  TGVDNVDLEAATRKGILVMNTP-NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWDRKKFMGTELNGK
          TGVDNVDLEAATRKGIL.MNTP.NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWD.KKFMGTELNGK
Retrocopy TGVDNVDLEAATRKGILPMNTP<NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWDQKKFMGTELNGK

Parental  TLGILGLGRIGREVATRMQSFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGL
          TLGILGL.RI.REVATRMQSFGMKTVGYDPIISPEVAASF.VQ.LPLEEIWPLCDFITVHTPLLPSTTGL
Retrocopy TLGILGLSRIRREVATRMQSFGMKTVGYDPIISPEVAASFDVQ*LPLEEIWPLCDFITVHTPLLPSTTGL

Parental  LNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGA
          LNDSTFAQCKKG.RVVNCARGG.VDEGALLRALQSGQCAGAALDVFTEEPP.DRALV.HE.VISCPHLGA
Retrocopy LNDSTFAQCKKGMRVVNCARGGTVDEGALLRALQSGQCAGAALDVFTEEPPQDRALVEHEKVISCPHLGA

Parental  STKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEAMGTLMHAWAGSPKGTIQV
          STKEAQS.CGEEIAVQFVDMVK.KSLT..VNAQALTSAFSPHTKPWI.LAEA.G.LMHAWAGSPKGTIQV
Retrocopy STKEAQSHCGEEIAVQFVDMVKEKSLTSTVNAQALTSAFSPHTKPWIDLAEALGMLMHAWAGSPKGTIQV

Parental  VTQGTSLKNA-GTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNPGVPGEQGSGECLLTV
          VTQGTSLKNA.GTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNPG.PGEQGSGECLLTV
Retrocopy VTQGTSLKNA>GTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNPGAPGEQGSGECLLTV

Parental  ALAGAPYQAV-GL-VQGTTPMLQMLNGAVFRPEVPLRRGQPLLVFRAQPSDPGMLPTMIGLLAEAGVQLL
          ALAG.PYQ.V.GL..QGTT.MLQMLNGAVFR.EVPLRRGQPLL.FRAQPS.P.MLPTMIGLLAEAGVQLL
Retrocopy ALAGDPYQVV>GL>IQGTTLMLQMLNGAVFRREVPLRRGQPLLKFRAQPSNPVMLPTMIGLLAEAGVQLL

Parental  SYQTSMVSDGEPWHVMGLSSLLPSLETWKQHVLEAFQFCF
          SYQTSMVSDGEP..V.GLSSLLPSLETWK.HVLE.FQFCF
Retrocopy SYQTSMVSDGEP*YVTGLSSLLPSLETWK*HVLEVFQFCF

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
SRP007412_brain	0.00 RPM	21.05 RPM
SRP007412_cerebellum	0.00 RPM	11.94 RPM
SRP007412_heart	0.00 RPM	0.59 RPM
SRP007412_kidney	0.00 RPM	5.64 RPM
SRP007412_liver	0.00 RPM	0.08 RPM
SRP007412_testis	4.16 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3021 was not detected

EST

No EST(s) were mapped for retro_mmus_3021 retrocopy.

TSS

No TSS is located nearby retro_mmus_3021 retrocopy 5' end.

Lab

retro_mmus_3021 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3021 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
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,