RetrogeneDB ID: retro_mmus_2169

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:65613588..65615183(+)
• 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_2169
ATGGCCTTCGCAAATCTGCGCAAAGTACTCATCAGTGACAGCCTGGACCCCTGCTGCTGGAAGATCCTGCAAGATGGAGG
GCTGCAGGTGGTGGAGAAGCAGAACTTGAGCAAGGAGGAGCTGATAGCTGAATTCTAGGACTGTGAAGGCCTCATTGTCC
GGTCAGCTACTAAGGTCACTGCTGATGTCATCAATGCAGCAGAGAATCTCCAGGTGGTGGGCAGGGCTGGCACAGGTATG
GACAATGTGGATCTGGAGGCTGTCACAAGGAAGGGCATCCTAGTCATGAACACCCCCAACGGGAACAGCCTCAGTGCTGT
GGAGCTCACCTGTGGGATGATCATGTGCCTGGCCAGGCAGATTCCCCAGGCAACGGCTTCGATGAAAGATGGCAAATGGG
ACCGGAAGAAGTTCATGGGGACAGAACTGAACGGGAAGACATTGGGAATTCTTGGCCTCGGCAGAATTGGAAGAGAGGTG
GCCACCCAGATGCAGTCCTTTGGAATGAAGACTGTAGGCTATGATCCCATCATCTCTCCTGAAGTTGCGGCCTCCTTTGG
TGTTCAGCAGCTGCCGCTAGAGGAGATCTGGCCTCTCTGTGACTTTATAACTGTCCATACCCCACTCCTGCCCTTCACCA
CAGGCTTACTGAATGACATCATCTTTGCTCAGTGCAAGAAAGGCGTGCGAGTGGTAAACTGTGCTCGAGGAGGCACTGTG
GATGAAGGTGCCATGCTGCATGCCCTGCAGTCTGGTCAGTGTGCTGGGGCTGCACTGGATGTGTTTACAGAAGAGCTACC
ACGGGACCGGGACTTAGTGGACCACGAGAATGTCATCAACTGTCCCCACCTGGGTGCCAGCACCAAGGAAGCTCAAAGCC
GTTGTGGGGAGGAAATCGCAGTCCAGTTTGTGGACATGGTGAAGGGGAAATCTTTAACAGGCGTCGTGAACGACCAGGCC
CTCACCAGTGCCTTCTCTCCACAGACCAAGCCTTGGATAGGTCTGGCAGAAGCATTGGGCACGCTGATGCACGCCTGGGC
TGACTCCCCTAAAGGGACCATCCAGGTGGTTACACAAGGAACATCTCTGAAGAATGCTGGGACCTGCCTGAGCCCTGCAG
TCATTGTCGGCCTTCTAAGAGAAGCATCTAAGCAGGCAGACGTGAACTTGGTGAACGCTAAGCTACTGGTGAAAGAGGCT
GGCCTCAATGTCACCACCTCCCACAACTCTGGGGTTCCAGGAGAGGAGGGCAGTGGGGAATGCCTCCCGACTGTGACCCT
GGCAGGTGCCCCCTACCAAGCTGTGGGCTTGGTCCAGGGCACCACACCAATGCTGCAGATGCCCAACGGAGCTGTCTTCA
GACCAGAGGTGCCACTACGCAGGGGCCAACCCCTGCTCATATTCCGGGCTCAGCCCTCCAACCCTGTGATGCTGCCCACT
ATGATCGGCCTCCTGGCAGAGGGAGGTTACAGCTGCTGTCCTACCAAACCTCCATGGTGTCTGACGGAGAGCCCTGGCAC
GTCATGGGCCTCTCCTCCCTGCTGCCCAGCCTGGAAACATGGAAGCAGCATGTATTGGAGGCTTTCCAGTTCTGC

Alignment

ORF - retro_mmus_2169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.0 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKL
          MAFANLRKVLISDSLDPCC.KILQDGGLQVVEKQNLSKEELIAE..DCEGLIVRSATKVTADVINAAE.L
Retrocopy MAFANLRKVLISDSLDPCCWKILQDGGLQVVEKQNLSKEELIAEF*DCEGLIVRSATKVTADVINAAENL

Parental  QVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWDRKKFMG
          QVVGRAGTG.DNVDLEA.TRKGILVMNTPNGNSLSA.ELTCGMIMCLARQIPQATASMKDGKWDRKKFMG
Retrocopy QVVGRAGTGMDNVDLEAVTRKGILVMNTPNGNSLSAVELTCGMIMCLARQIPQATASMKDGKWDRKKFMG

Parental  TELNGKTLGILGLGRIGREVATRMQSFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLL
          TELNGKTLGILGLGRIGREVAT.MQSFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLL
Retrocopy TELNGKTLGILGLGRIGREVATQMQSFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLL

Parental  PSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVIS
          P.TTGLLND..FAQCKKGVRVVNCARGG.VDEGA.L.ALQSGQCAGAALDVFTEE.PRDR.LVDHENVI.
Retrocopy PFTTGLLNDIIFAQCKKGVRVVNCARGGTVDEGAMLHALQSGQCAGAALDVFTEELPRDRDLVDHENVIN

Parental  CPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEAMGTLMHAWAGSP
          CPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVN.QALTSAFSP.TKPWIGLAEA.GTLMHAWA.SP
Retrocopy CPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNDQALTSAFSPQTKPWIGLAEALGTLMHAWADSP

Parental  KGTIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNPGVPGEQGSGE
          KGTIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHN.GVPGE.GSGE
Retrocopy KGTIQVVTQGTSLKNAGTCLSPAVIVGLLREASKQADVNLVNAKLLVKEAGLNVTTSHNSGVPGEEGSGE

Parental  CLLTVALAGAPYQAVGLVQGTTPMLQMLNGAVFRPEVPLRRGQPLLVFRAQPSDPGMLPTMIGLLAEAG-
          CL.TV.LAGAPYQAVGLVQGTTPMLQM.NGAVFRPEVPLRRGQPLL.FRAQPS.P.MLPTMIGLLAE.G.
Retrocopy CLPTVTLAGAPYQAVGLVQGTTPMLQMPNGAVFRPEVPLRRGQPLLIFRAQPSNPVMLPTMIGLLAEGG<

Parental  VQLLSYQTSMVSDGEPWHVMGLSSLLPSLETWKQHVLEAFQFC
          .QLLSYQTSMVSDGEPWHVMGLSSLLPSLETWKQHVLEAFQFC
Retrocopy LQLLSYQTSMVSDGEPWHVMGLSSLLPSLETWKQHVLEAFQFC

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	0.02 RPM	5.64 RPM
SRP007412_liver	0.00 RPM	0.08 RPM
SRP007412_testis	2.20 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2169 was not detected

EST

1 EST(s) were mapped to retro_mmus_2169 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI642727	65614315	65614703	95.1	374	13	359

TSS

No TSS is located nearby retro_mmus_2169 retrocopy 5' end.

Lab

retro_mmus_2169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2169 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,