RetrogeneDB ID: retro_mmus_1708

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:36920399..36921514(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000063514
• Aliases: Gm6756, EG627427
• 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_1708
GCCTTCACAAATCTGCGCAAAGTACTCATCAGTGACAGCCTGGACCCCTGCTGCTGGAAGATCCTGCAAGATGGAGAGCT
GCAGGTGGTGGAGAAGCAGAACTTGAGCAGGAGGAGCTGATAGCTGAACTCCAGGACTGTGAAGGCCTCATTGTCCGGTC
AGCTACTAAGGTCACTGCTGATGTCATCAATGCAGCAGAGAAGCTCCAGGTGATGGGCAGGGCTGGCACAGGCGTGGACA
ATGTGGATCTGGAGGCTGCCACGAGGAAGGGCATCCTAGTCATGAACACCCCCAACTGGAACAGCCTCAGTGCTGTGGAG
CTCACCTGTGGGATGATCATGTGCCTGGCCAGGCAGATTCCCCAGGCAACGGCTTCGATGAAAGATGGCAAATGGGACCA
GAAGAAGTTCATGGGGACAGAACTGAACGGGAAGACACTGGGAATTCTTGGCCTCGGCAGAATCAGAAGAGAGGTGGCCA
CCCGAATGCAGTCCTTCGGAATGAAGACTGTAGGCTATGACCCCATCATCTCTCCTGAAGTTGCGGCCTCCTTTGGTGTT
CAGCAGCTGCCGCTGGTGGAGATCTGGCCTCTCCATGACTTCATAATTGTCCATACCCCACTCCTGCCCTCCACCACAGG
CTTGTTGAATGACAGCACCTTTGCTCAGTGCAAGAAAGGCGTGTGAGTGATGAACTGTGCTCGAGGAGGCATTGTGGATG
AAGGTGCCCTGCTCTGAGTCCTGCAGTCTGGTCAGTGTGCTGGGGCTGCACTGGATGTGTTTACAGAAGAGCCACCACTG
GACTGGGCCTTAGTGGACCACGAGAATGTCATCAGCTGTCCCCACCTGGGTGCCAGCATCAAGGAAGCCCAGAGCCGCTG
TGGGGAGGAAATAGCAGTCCTGTTTGTGGGAATGGTGAAGGGGAAATCTCTAACAGGTGTCGTGAACGCCCAGGCCCTCA
CCAGTGCCTTCTCTCCACACACCAAGCCTTGGATTGGCCTGGCAGAAGCATTAGGCACACTGATGCACGCCTGGGCTGGC
TCCCCTAAAGAGACCATCCAGGTGGTTACACAAGGGCAACCTTCTGTGTCCCCAGAAACGTTTCTGAAGAATGCT

Alignment

ORF - retro_mmus_1708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.88 %
• Parental protein coverage: 69.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSK-EELIAELQDCEGLIVRSATKVTADVINAAEKL
          AF.NLRKVLISDSLDPCC.KILQDG.LQVVEKQNLS..EELIAELQDCEGLIVRSATKVTADVINAAEKL
Retrocopy AFTNLRKVLISDSLDPCCWKILQDGELQVVEKQNLSR<EELIAELQDCEGLIVRSATKVTADVINAAEKL

Parental  QVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWDRKKFMG
          QV.GRAGTGVDNVDLEAATRKGILVMNTPN.NSLSA.ELTCGMIMCLARQIPQATASMKDGKWD.KKFMG
Retrocopy QVMGRAGTGVDNVDLEAATRKGILVMNTPNWNSLSAVELTCGMIMCLARQIPQATASMKDGKWDQKKFMG

Parental  TELNGKTLGILGLGRIGREVATRMQSFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLL
          TELNGKTLGILGLGRI.REVATRMQSFGMKTVGYDPIISPEVAASFGVQQLPL.EIWPL.DFI.VHTPLL
Retrocopy TELNGKTLGILGLGRIRREVATRMQSFGMKTVGYDPIISPEVAASFGVQQLPLVEIWPLHDFIIVHTPLL

Parental  PSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVIS
          PSTTGLLNDSTFAQCKKGV.V.NCARGGIVDEGALL..LQSGQCAGAALDVFTEEPP.D.ALVDHENVIS
Retrocopy PSTTGLLNDSTFAQCKKGV*VMNCARGGIVDEGALL*VLQSGQCAGAALDVFTEEPPLDWALVDHENVIS

Parental  CPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEAMGTLMHAWAGSP
          CPHLGAS.KEAQSRCGEEIAV.FV.MVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEA.GTLMHAWAGSP
Retrocopy CPHLGASIKEAQSRCGEEIAVLFVGMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMHAWAGSP

Parental  KGTIQVVTQGTSLKNAGTCLSPA
          K.TIQVVTQG.......T.L..A
Retrocopy KETIQVVTQGQPSVSPETFLKNA

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	0.21 RPM	21.05 RPM
SRP007412_cerebellum	0.30 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	2.24 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1708 was not detected

EST

No EST(s) were mapped for retro_mmus_1708 retrocopy.

TSS

No TSS is located nearby retro_mmus_1708 retrocopy 5' end.

Lab

retro_mmus_1708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1708 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,