RetrogeneDB ID: retro_rnor_452

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:80934512..80935680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Phgdh
• Ensembl ID: ENSRNOG00000019328
• Aliases: None
• Description: D-3-phosphoglycerate dehydrogenase [Source:UniProtKB/Swiss-Prot;Acc:O08651]

Sequence

>retro_rnor_452
AAGCAGAACTTGAGCAAGGAGGAGCTGATAGCCGGACTACGGGACTGTGAAGGCCTTATCATCTGGTCAGCTACTAAGGT
CGTTGCTGATGTTATCAACACAGCAGAGAAGCTCCAGGTGGTGGGCAGGGCTGAGACAGGTGTGGACAATGTGGATCTGG
AGACTGCCACGAGGAAGGGCATCCTAGTCATGAACACCCCTAATGGAAACAACCTCAGTGCTGCAGAACTCACCTGTGGG
ATGATCATGTGACTGGCCAGGCAGATCCCCCAGGCAGCGGTGTCAATGAAAGATGACAAATGAGACCAGAAGAAGTTCAT
GGGGACAGAACTGAATGGGATGACACTGGGAATTCTTGGCCTAGGCAGAATTGGAAGAGAGGTGGCTACCTGAATGTAGT
CCTTTGGATGAAGACTGTAGGCTATATCCCCATCAATTCTCCAGAAGTTGCTGCCTCCTTTGGTGTTCAGCACCTGGCAC
TAGAGGAGATCTGGCCTCTCTGTGATTTCATCACTGTCCACATCACACTCCTGCCCTCCACCACAGGCTTGCTCAATGAT
AGAACCTTTGCCCAGTGCAAGAAAGGCCTGCGAGTGGTGAACTGTGCTCGAGGAGGTATCATGGATGAAGGTGCCCTGAT
CCATGCCCTGCAGTCTGGTCAGTATGCTGGGATGCATTGGATGTGTTTACAGAAAAGCCACCACAGGACCAGGCCTTAGT
AGACCACAAGAATGTGATCAGCTGTCCCTACGTGGGCGCCAGCACAAAGGAGGCCCAGAGCCGCTGTGGGGAGGAAATGG
CAGTCCAGTTTGTGGACATAGTGAAGGGGAAATCTCTAACAGGGGTTGTAAGTGCCCAGGTCCTTACCAGTGCCTTCTCG
TCACACACCAAGCCTTATATTGGTCTGGCAGAAGCATTGGGCATGCTGATGCACTCCTGGGCTGGCTCCCCTAAAGGGTC
CATCCAGGTGGTTACACAAGGAACATCTCTGAAGAATACTGGGACCTGCCTGAGCCCTACAGTCATTGTCGGCCTTCTGA
GAGAAGCATCAAAGCAGGTAGATGTGAACTTGATGAATGCTAAGCTACGTGGGAAAGAGGCTGCCCTCAGTGTCACCACC
TCCCACAGTCCTGGGGTTCCAGGGGAGCAGGGCAATGGGGAAGGCCTC

Alignment

ORF - retro_rnor_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.18 %
• Parental protein coverage: 73.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGVLVMNTPNGN
          KQNLSKEELIA.L.DCEGLI..SATKV.ADVIN.AEKLQVVGRA.TGVDNVDLE.ATRKG.LVMNTPNGN
Retrocopy KQNLSKEELIAGLRDCEGLIIWSATKVVADVINTAEKLQVVGRAETGVDNVDLETATRKGILVMNTPNGN

Parental  SLSAAELTCGMLMCLARQIPQATASMKDGKWDRKKFMGTELNGKTLGILGLGRIGREVAARMQAFG-MKT
          .LSAAELTCGM.M.LARQIPQA..SMKD.K.D.KKFMGTELNG.TLGILGLGRIGREVA..M..FG.MKT
Retrocopy NLSAAELTCGMIM*LARQIPQAAVSMKDDK*DQKKFMGTELNGMTLGILGLGRIGREVAT*M*SFG<MKT

Parental  VGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIVD
          VGY.PI.SPEVAASFGVQ.L.LEEIWPLCDFITVH..LLPSTTGLLND.TFAQCKKG.RVVNCARGGI.D
Retrocopy VGYIPINSPEVAASFGVQHLALEEIWPLCDFITVHITLLPSTTGLLNDRTFAQCKKGLRVVNCARGGIMD

Parental  EGALLRALQSGQCAGA-ALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDMVKGK
          EGAL..ALQSGQ.AG..ALDVFTE.PP.D.ALVDH.NVISCP..GASTKEAQSRCGEE.AVQFVD.VKGK
Retrocopy EGALIHALQSGQYAGM<ALDVFTEKPPQDQALVDHKNVISCPYVGASTKEAQSRCGEEMAVQFVDIVKGK

Parental  SLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMHAWAGSPKGTIQVVTQGTSLKNAGTCLSPAVIVGLLR
          SLTGVV.AQ.LTSAFS.HTKP.IGLAEALG.LMH.WAGSPKG.IQVVTQGTSLKN.GTCLSP.VIVGLLR
Retrocopy SLTGVVSAQVLTSAFSSHTKPYIGLAEALGMLMHSWAGSPKGSIQVVTQGTSLKNTGTCLSPTVIVGLLR

Parental  EASKQADVNLVNAKLLVKEAGLNVTTSHSPGVPGEQGIGECL
          EASKQ.DVNL.NAKL..KEA.L.VTTSHSPGVPGEQG.GE.L
Retrocopy EASKQVDVNLMNAKLRGKEAALSVTTSHSPGVPGEQGNGEGL

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
SRP017611_brain	0.00 RPM	43.28 RPM
SRP017611_kidney	0.00 RPM	78.37 RPM
SRP017611_liver	0.00 RPM	1.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_452 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_452 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 ,