RetrogeneDB ID: retro_mmus_3176

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:13745876..13747480(-)
• 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_3176
ATGGCCTTCGCAAATCTGCGCAAAGCACTCATCAGTGACAGCCTGGACCCCTACTTCCACTTCCGGAAGATCCTGCAAGA
TGGAGGGCTGCAGGTGGTGGAGAAGCAGAACTTGAGCAAGGAGGAGCTGATAGCTGAACTCCAGGACTGTGGAGGCCTCA
TTGTCCGGTCAGCTACCAAGGTCACTGCTGATGTCATCAGTGCAGCAGAGAAGCTCCAGGTGGTGGGCAGGGCTGGCACA
GGCGTGGACAATGTGGATCTGGAGGCTGCCACGAGGAAGGGCATCCTAGTCATGAACACCCCCAACGTGAACAGCCTCAG
TGCTGAGGAACTCACCTGTGGGATGATCATGTGCCTGGCCAGGCAGATTCCCCAGGCAACGGCTTGGATGAAAGATGGCA
AATGGGACCAGAAGAAGTTCATGGGGACAGAACTGAACGGGATGACACTGGGAATTCTTGGCCTCGGCAGAATCAGAAGA
GAGGTGGCCACCGTAATGCAGTCCTTTGGAATGAATACTGTAGGCTATGACCCCATCATCTCTCCTAAGTCTCTGCCTCC
TTTGGTGTTCAGCAGCTGCCGCTGGAGGAGATCTGGCCTCTCTGTGACTTTATAACTGTCCATACCCCACTCCTGCCCTC
TACCACAGGCTTGCTGAATGACAGCACCTTTGCTCAGTGCAAGAAAGTCGTGCGAGTGGTGAACTGTGCTCGAGGAGGCA
TCGTGGATGAAGGTGCCCTGCCGCGTGCCCTGCAGTCTGGTCAGTGTGCTGGGGCTGCACTGGATGTGTTTACAGAAGAG
CCGCCACGGGACCAGGCCTTAGTGGACCACGAGAATGTCATCAGCTGTCCCCACCTGGGTGCCAGCACCAAGGAAGCCCA
GAGCTGCTGTGGGGAGGAAATCGTAGTCCAGTTTGTGGACATGGTGAAGGGGAAATCTCTAACAGGTGTCGTGAACGCCC
AGGCCCTCACCAGTGCCTTCTCTCCACACACCAAGCCTTGGATTGATCTGGCAGAAGCAATGGGCATGCTGATGCATGCC
TGGGCTGACTCCCCTAAAGGGACCATCCAGGTGGTTGCACAAGGAACATCTCTGAAGAATGCTGGGACCTGCCTGAGCCC
TGCAGTCATTGTCGGCCTTCTGAGAGAAGCATCTAAGCAGACAGACATGAACTTGGTGAACGCTAAGCTACTGGTGAAAG
AGGCTGGCCTCAATGTCACCACCTCCCACAACCCTGGGGTTCCAGGGGAGCAGGGCAGCGGGGAATGCCTCCTGACTGTG
GCCCTGGCAGGTGCCCCCTACCAAGCTGTGGGCTTGGTCCAGGGCACCACACCAATGCTGCAGATGCTCAACAGAGCTGT
CTTCAGACCAGAGGTGCCACTACGCAGGTGCCAACCCCTGCTCATATTCCGGGCTCAGCCCTCTAACTGTGTGATGGTGC
CCACTATGATTGGCCTCTTGGCAGAGGGGGGTGTATAGCTGCTGTCCTACCAAACCTCCATGGTGTCTGACGGAGAGCCC
TGGCACGTCACGGGCCTCTCCTCCCTGCTGCCCAGCCTGGAAACAAGGAAGCAGCATGTATTGGAGGCTTTCCAGTTCTG
CTTC

Alignment

ORF - retro_mmus_3176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFANLRKVLISDSLDPCC--RKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAE
          MAFANLRK.LISDSLDP....RKILQDGGLQVVEKQNLSKEELIAELQDC.GLIVRSATKVTADVI.AAE
Retrocopy MAFANLRKALISDSLDPYFHFRKILQDGGLQVVEKQNLSKEELIAELQDCGGLIVRSATKVTADVISAAE

Parental  KLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWDRKKF
          KLQVVGRAGTGVDNVDLEAATRKGILVMNTPN.NSLSA.ELTCGMIMCLARQIPQATA.MKDGKWD.KKF
Retrocopy KLQVVGRAGTGVDNVDLEAATRKGILVMNTPNVNSLSAEELTCGMIMCLARQIPQATAWMKDGKWDQKKF

Parental  MGTELNGKTLGILGLGRIGREVATRMQSFGMKTVGYDPIISPE-VAASFGVQQLPLEEIWPLCDFITVHT
          MGTELNG.TLGILGLGRI.REVAT.MQSFGM.TVGYDPIISP..V.ASFGVQQLPLEEIWPLCDFITVHT
Retrocopy MGTELNGMTLGILGLGRIRREVATVMQSFGMNTVGYDPIISPK<VSASFGVQQLPLEEIWPLCDFITVHT

Parental  PLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHEN
          PLLPSTTGLLNDSTFAQCKK.VRVVNCARGGIVDEGAL.RALQSGQCAGAALDVFTEEPPRD.ALVDHEN
Retrocopy PLLPSTTGLLNDSTFAQCKKVVRVVNCARGGIVDEGALPRALQSGQCAGAALDVFTEEPPRDQALVDHEN

Parental  VISCPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEAMGTLMHAWA
          VISCPHLGASTKEAQS.CGEEI.VQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWI.LAEAMG.LMHAWA
Retrocopy VISCPHLGASTKEAQSCCGEEIVVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIDLAEAMGMLMHAWA

Parental  GSPKGTIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNPGVPGEQG
          .SPKGTIQVV.QGTSLKNAGTCLSPAVIVGLLREASKQ.D.NLVNAKLLVKEAGLNVTTSHNPGVPGEQG
Retrocopy DSPKGTIQVVAQGTSLKNAGTCLSPAVIVGLLREASKQTDMNLVNAKLLVKEAGLNVTTSHNPGVPGEQG

Parental  SGECLLTVALAGAPYQAVGLVQGTTPMLQMLNGAVFRPEVPLRRGQPLLVFRAQPSDPGMLPTMIGLLAE
          SGECLLTVALAGAPYQAVGLVQGTTPMLQMLN.AVFRPEVPLRR.QPLL.FRAQPS...M.PTMIGLLAE
Retrocopy SGECLLTVALAGAPYQAVGLVQGTTPMLQMLNRAVFRPEVPLRRCQPLLIFRAQPSNCVMVPTMIGLLAE

Parental  AGVQLLSYQTSMVSDGEPWHVMGLSSLLPSLETWKQHVLEAFQFCF
          .GV.LLSYQTSMVSDGEPWHV.GLSSLLPSLET.KQHVLEAFQFCF
Retrocopy GGV*LLSYQTSMVSDGEPWHVTGLSSLLPSLETRKQHVLEAFQFCF

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	0.12 RPM	21.05 RPM
SRP007412_cerebellum	0.09 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	0.46 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3176 was not detected

EST

No EST(s) were mapped for retro_mmus_3176 retrocopy.

TSS

No TSS is located nearby retro_mmus_3176 retrocopy 5' end.

Lab

retro_mmus_3176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3176 has 0 orthologous retrocopies within eutheria group .

---

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,