RetrogeneDB ID: retro_mmus_2057

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:87199929..87201525(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081168
• 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_2057
ATGCCCTTAGCAAATCTGTGCAATGTACTGTTCAGTGACAGCCTGGACCCCTGCTGCCGGATGATCATGCAAGATGGAGG
GCTGCAGGTGGTGGAGAAGCCAAACGAGCAAAGGAGGAACTTATAGCTGAACTCCAGGACTGTGAAGACTTATCGTTCAG
TCAGCTACTAAGGTCACTGCTGGTGTCATCAATGTAGCAGAGAAGTTCCAGGTGGTAGGCAGGGCTGGTACCGGCGTGGA
CAATGTGGATCTGGAGGCTGCCACAAGGAAGAGTATTTTAGTCATGAACACCCCCACGGAAACAGCATCAATGCTGTGGA
GCTCATCTGTGGAATGATCATGTGCCTGGCCAGGCAGATTCCCCAGGTGACTGCTTCGATGAAAGATGGCAAATGGGACC
AGAAGTTCATGGGGACAGAACTGAACGGGAAGACACTGGGAATTCTTGGCCTAGGTAGAATCAGAAGACAGGTGGCCATG
GGAATACAGTCCTTTGGAATGAAAACTGTAGGCTATGACCCCATCATTTCTCCTGAAGCCACAGCCTCCTTTTGTGTTCA
GCAGTTGCCGCAGGAGGAGATCTGGCATCTCTGTGACTTCATTACTGTCCATACCCCACTCTTGCCCTCCACCACAGGCT
TGCTGAATAACAGCACTTTGCTCAGTGCAAGAAAGGTGTGTGAGTGGTGAACTGTGCTCAAGGAGGCATTGTGGATGAAG
GTGCCCTGTTCCTGTTGCGTGCCCTGCAGTCTGGTCAGTGTGCTGGGGCTTCACTGGATGTGTTTACAGAAGAGCCACCA
AGGGACCTGGATTTAGTGGACCATGAGAACGTCATCAACTGTCCCCTCCTGGGTGCCAGCACCAAGGAAGCCCAGAGCCA
CTGTGCAGAGAAATCATAGTCCAGTTTGTGGACATGGTGAAGAGGAATTCTCTAACAGGGGTCGTGAATGCCCAGGCCCT
TACCAGTGTCTTCTCTCCAAACTCCAAGCCTTGCATTGGTCTGACAGAAGCACTGGGCATGCTGATGCACTCCTGGGCTG
GCTCCCCTAAATGGACCATCCAGGTGGTTACACAAGGAACATCTCTGAAGAATGCTGGGACCTGCCTGAGCCCTGCAGTC
ATTGTCGGCCTTCTGAGAGAAGCATCCAAGCAGGCAGATGTGAACTTGGTGAATGCTAAGCTACTGGTGAAAGAGGCTGG
CCTCAATGTCACCACCTCCCACAACCCTGCGGTCCCAGGGGAGCAGGGCAGCAGGGAATGCCTCCTGACTGTGGCCCTAG
CAGGTGTCTCCTACCAAGCTGTGGGCTTGGTCAGGGCACCACACCAATACTGCAGGTGCTCAACAGAGCTGTCTTCAGAC
CAGAGCTGCCCCTACACAGGGGCCAACCCCTGCTTATGTTCCGGGCTCAGCCCTTCAACCCTGTGATGCTGCCTACTATG
ATCGGTCTCCTGGCAGAGGCGGTTGTACAGCTGCTGTCCTACAAAACCTCCAAGGTGTCTGACAGAGAGCCCTGGCATGT
CATGAGCCTCTCCTCCATGCTGCCCAGCCTGGAAGCCTGGAAGCAGCCTGTATCTGAGGCTTTAAAGTTCTGCTTC

Alignment

ORF - retro_mmus_2057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQN-LSKEELIAELQDCEGL-IVRSATKVTADVINAAE
          M..ANL..VL.SDSLDPCCR.I.QDGGLQVVEK.N...KEELIAELQDCE.L.IV.SATKVTA.VIN.AE
Retrocopy MPLANLCNVLFSDSLDPCCRMIMQDGGLQVVEKPN<RAKEELIAELQDCEDL<IVQSATKVTAGVINVAE

Parental  KLQVVGRAGTGVDNVDLEAATRKGILVMNTP-NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWDRKK
          K.QVVGRAGTGVDNVDLEAATRK.ILVMNTP..GNS..A.EL.CGMIMCLARQIPQ.TASMKDGKWD.K.
Retrocopy KFQVVGRAGTGVDNVDLEAATRKSILVMNTP<HGNSINAVELICGMIMCLARQIPQVTASMKDGKWDQK-

Parental  FMGTELNGKTLGILGLGRIGREVATRMQSFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHT
          FMGTELNGKTLGILGLGRI.R.VA...QSFGMKTVGYDPIISPE..ASF.VQQLP.EEIW.LCDFITVHT
Retrocopy FMGTELNGKTLGILGLGRIRRQVAMGIQSFGMKTVGYDPIISPEATASFCVQQLPQEEIWHLCDFITVHT

Parental  PLLPSTTGLLNDST-FAQCKKGVRVVNCARGGIVDEGAL--LRALQSGQCAGAALDVFTEEPPRDRALVD
          PLLPSTTGLLN.ST.FAQCKKGV.VVNCA.GGIVDEGAL..LRALQSGQCAGA.LDVFTEEPPRD..LVD
Retrocopy PLLPSTTGLLNNST<FAQCKKGV*VVNCAQGGIVDEGALFLLRALQSGQCAGASLDVFTEEPPRDLDLVD

Parental  HENVISCPHLGASTKEAQSRCGE-EIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEAMGTLM
          HENVI.CP.LGASTKEAQS.C.E.EI.VQFVDMVK..SLTGVVNAQALTS.FSP..KP.IGL.EA.G.LM
Retrocopy HENVINCPLLGASTKEAQSHCAE<EIIVQFVDMVKRNSLTGVVNAQALTSVFSPNSKPCIGLTEALGMLM

Parental  HAWAGSPKGTIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNPGVP
          H.WAGSPK.TIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNP.VP
Retrocopy HSWAGSPKWTIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNPAVP

Parental  GEQGSGECLLTVALAGAPYQAVGLV-QGTTPMLQMLNGAVFRPEVPLRRGQPLLVFRAQPSDPGMLPTMI
          GEQGS.ECLLTVALAG..YQAVGLV.QGTTP.LQ.LN.AVFRPE.PL.RGQPLL.FRAQP..P.MLPTMI
Retrocopy GEQGSRECLLTVALAGVSYQAVGLV<QGTTPILQVLNRAVFRPELPLHRGQPLLMFRAQPFNPVMLPTMI

Parental  GLLAEAGVQLLSYQTSMVSDGEPWHVMGLSSLLPSLETWKQHVLEAFQFCF
          GLLAEA.VQLLSY.TS.VSD.EPWHVM.LSS.LPSLE.WKQ.V.EA..FCF
Retrocopy GLLAEAVVQLLSYKTSKVSDREPWHVMSLSSMLPSLEAWKQPVSEALKFCF

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	0.00 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2057 was not detected

EST

No EST(s) were mapped for retro_mmus_2057 retrocopy.

TSS

No TSS is located nearby retro_mmus_2057 retrocopy 5' end.

Lab

retro_mmus_2057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2057 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,