RetrogeneDB ID: retro_mmus_1008

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:48312790..48314251(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_1008
GCTGAACTTTAGGACTGTGAAGGCCTTATCATCCGGTCAGCTACTAAGGTCACTGCTGATGCCATCAATGCAGCAGGGAA
GCTCCAGTTGGTGGGCAAGGCTGGTACAGGCGTGGACAATGTGAATCTGGAGGCTGCCACGAGGAAGGGCATCTTACTCA
TGAACACCCCCAATGGAAACAGCCTCAGTACTGCGGAGCTCACCTGAGGGATGATCATGTGCCCAGCCAGGCAGATTCCC
CAGGCAACGGCTTCGATGAAAGATGGCACATGAGACCAGAAGAATTTAATGGGGGACAGAACTGAACGGGAAGACACTGG
GAATTCTTGGCCTAGGCAGAATCGGAAGAGAGGTGGCCACCCAAATGCAGTCCTTTGGAATGAAGACTGTAGGCTATGAC
CCCATCATTTCTCCTGAAGTTGCGACCTCCTTTGGTGTTCAGCAGCTGTCGCTGGAGGAGATCTGACCTCTCTGTGACTT
CATAACTGTCCCTTTCCCACTCCTGCCCTCCACCACAAGCTTGCTGAATGACAGCACCTTTGCTCAGTGCAAGAAAGGTA
TGTGAGTAGTGAACTGTGCTCGAGGAGGCATTGTGGATGAAGGTGCCCTGCAGTCTGGTTAGTGTGCTGGAGATGCACTG
GATGTGATTACAGAAGAGCCATCATGGGACCCAGCCTTAGTGGACCGTGAGAACATCATCAGCTGTCCCCAACTGGGTGC
CAGCACCAAGGAAGCCCAGAGCCACTGTGGGGAGGAAATCACAGTCCAGTTTGTGGACATGGTGAAGGGGAAATCTCTAA
CAGGGGTCGTGAACGCCCAGGCCCTTACCAGTGCCTTCTCTCCACACACCAAGCCTTGGATTGGTCTGGCAGAAGCATTG
GACATGCTGATGCATCCCTGGGCTGGCTCCCCTAAAGGGACCATCCAAGTGGTTACACAAGGAACATCTCTGAAGAATGC
TGGGACCTGCCTGAGCCCTGCAGTCATTGTCAGCCTTCTCAGAGAAGCATCCAAGCAGGCAGACACGAACTTGGTGAACG
CTAAGCTACTGGTGAAAGAGGCTGGCTTCAATGTCACCACCTCCCACAACCCTGGGGGCCCAGGGGAGCAGGGCAACAGG
GAATGCCTCCTGACTCTGGCCCTGGCAGGTACCCCCTACCAAGGTGTAGGCTTGGTCCAGGGCACCATACCAATGCTGCA
GGTGCTCAATGGAGCTGTCTTCAGACCAGAGGTGCCACTACGCAGGGGCCAACCCCTACTCATATTCCGGGCTCAGCCTT
CTAACCCTGTGATGCTGCCCATGATGATCGGCCTCCTGGCAGAGGCGGGTGTACAGCTGCTGTCCTACCAAACCTTCAAG
GTGTCTGACGGAGAGCCCTGGCATGTCATGGTCTCTCCTCCCTGCTGTCCAGCATGAAAGCATGGAAGCAGCACATATCA
GAGGCTTTCCAGATCTGCTTC

Alignment

ORF - retro_mmus_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 92.12 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCG
          AEL.DCEGLI.RSATKVTAD.INAA.KLQ.VG.AGTGVDNV.LEAATRKGIL.MNTPNGNSLS.AELT.G
Retrocopy AEL*DCEGLIIRSATKVTADAINAAGKLQLVGKAGTGVDNVNLEAATRKGILLMNTPNGNSLSTAELT*G

Parental  MIMCLARQIPQATASMKDGKWDRKKFMG-TELNGKTLGILGLGRIGREVATRMQSFGMKTVGYDPIISPE
          MIMC.ARQIPQATASMKDG..D.K..MG.TELNGKTLGILGLGRIGREVAT.MQSFGMKTVGYDPIISPE
Retrocopy MIMCPARQIPQATASMKDGT*DQKNLMG>TELNGKTLGILGLGRIGREVATQMQSFGMKTVGYDPIISPE

Parental  VAASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQS
          VA.SFGVQQL.LEEI.PLCDFITV..PLLPSTT.LLNDSTFAQCKKG..VVNCARGGIVDEG....ALQS
Retrocopy VATSFGVQQLSLEEI*PLCDFITVPFPLLPSTTSLLNDSTFAQCKKGM*VVNCARGGIVDEG----ALQS

Parental  GQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQAL
          G.CAG.ALDV.TEEP..D.ALVD.EN.ISCP.LGASTKEAQS.CGEEI.VQFVDMVKGKSLTGVVNAQAL
Retrocopy G*CAGDALDVITEEPSWDPALVDRENIISCPQLGASTKEAQSHCGEEITVQFVDMVKGKSLTGVVNAQAL

Parental  TSAFSPHTKPWIGLAEAMGTLMHAWAGSPKGTIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLV
          TSAFSPHTKPWIGLAEA...LMH.WAGSPKGTIQVVTQGTSLKNAGTCLSPAVIV.LLREASKQAD.NLV
Retrocopy TSAFSPHTKPWIGLAEALDMLMHPWAGSPKGTIQVVTQGTSLKNAGTCLSPAVIVSLLREASKQADTNLV

Parental  NAKLLVKEAGLNVTTSHNPGVPGEQGSGECLLTVALAGAPYQAVGLVQGTTPMLQMLNGAVFRPEVPLRR
          NAKLLVKEAG.NVTTSHNPG.PGEQG..ECLLT.ALAG.PYQ.VGLVQGT.PMLQ.LNGAVFRPEVPLRR
Retrocopy NAKLLVKEAGFNVTTSHNPGGPGEQGNRECLLTLALAGTPYQGVGLVQGTIPMLQVLNGAVFRPEVPLRR

Parental  GQPLLVFRAQPSDPGMLPTMIGLLAEAGVQLLSYQTSMVSDGEPWHVM-GLSSLLPSLETWKQHVLEAFQ
          GQPLL.FRAQPS.P.MLP.MIGLLAEAGVQLLSYQT..VSDGEPWHVM.GLSSLL.S...WKQH..EAFQ
Retrocopy GQPLLIFRAQPSNPVMLPMMIGLLAEAGVQLLSYQTFKVSDGEPWHVM<GLSSLLSSMKAWKQHISEAFQ

Parental  FCF
          .CF
Retrocopy ICF

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	0.14 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1008 was not detected

EST

No EST(s) were mapped for retro_mmus_1008 retrocopy.

TSS

No TSS is located nearby retro_mmus_1008 retrocopy 5' end.

Lab

retro_mmus_1008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1008 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,