RetrogeneDB ID: retro_mmus_1348

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:60392117..60393170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gpd1l
• Ensembl ID: ENSMUSG00000050627
• Aliases: Gpd1l, 2210409H23Rik, D9Ertd660e
• Description: glycerol-3-phosphate dehydrogenase 1-like [Source:MGI Symbol;Acc:MGI:1289257]

Sequence

>retro_mmus_1348
ATGGCTGCTGCAAGTCTGAAAGTGTGCATTGTGGGCTCCTGGAATTGGGGATCAGCTATTGCAAAAATAATTGGGACTAA
CGTCAAGAACCAGCAGAAGTTCCCCTCCACAGTCAAGATGTGGGTCTCTGAAGAAGCAGAGAACAGGGGGAAGCTGACAG
ATATCATAAATCACTCCCACAAAAACGTCAAATGTCTCCCAGGACACAAGCTGCCAGAAAATGTGGTTTCGGTCCCAAAT
CTCAGTGGGGCAGTGCAGGATGCAGGCCTGCTGGTGTTCACCACCCCACACAAGCTCATTCACAAAATCTGTAATGAGAT
TACTGGCAGGGTGCCCAAGAAGGCTCTCCGTATTATCCACACAGAGGGCATAGATGAGGGCCCAGGAGGGCTGATGCTCA
GCTCTGACATCATTCGAGAGAAGATAGGGATGGACGTCAGCGTGCTGATGGGGGCTAATACAGTCAGAGTGGTGGCCGCT
GGGGAGTTTTGTGAGACTACCATTGGTAGCAAAGTCATTCAGAATGGCATTCTCTTCAAAGAGCTGCTACAGACCCCCAA
CTTCTGCATCACTGTGGTGGATGATGCTGATGATGTGGAACTCTGCGGAGCACTAAAACACATTGTTGCTATGGGAACCA
CCTTCTGCGATGGCCTCCACTGTGGGAACAATGGTAAGGCTGCCATCACCCACCTTGGTCTTGTAGAACTGGTCACTTTC
ACTAGGATCTTCTGCAAGAGCCAGGTGTCTATGGCCACCTTCCTTGAGAGTTGTGGCTTGGCCAACCTCATCACTACCTG
CTATAGAGGGAATGACTAAAAAGTAGCTAAGACCTTCCTCAAGACTGGGGAGACTATTAGAAAATTAGAAAAGGAAATGC
TGAATGGTCAGGCACTTCAAGGACTTGAGATCTCTGCTTTAGTGTACCAATTCCTCAAGCAGAAGGGGCTTCTAGCTAAA
TTTCCATGATTCATAACAGTATATTGGATCTGCTATGAAGGCAAACCTCTCACAGAGATATTAACCTGCCTCCTGAGCCA
TCCTGCACATGTA

Alignment

ORF - retro_mmus_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAPLKVCIVGSGNWGSAVAKIIGSNVKTLQKFSSTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHK
          MAAA.LKVCIVGS.NWGSA.AKIIG.NVK..QKF.STVKMWV.EE..N..KLTDIIN..H.NVK.LPGHK
Retrocopy MAAASLKVCIVGSWNWGSAIAKIIGTNVKNQQKFPSTVKMWVSEEAENRGKLTDIINHSHKNVKCLPGHK

Parental  LPENVVAVPNLSEAVQDADLLVFVIPHQFIHKICDEITGRVPEKALGITLIKGIDEGPDGLKLISDIIRE
          LPENVV.VPNLS.AVQDA.LLVF..PH..IHKIC.EITGRVP.KAL.I....GIDEGP.GL.L.SDIIRE
Retrocopy LPENVVSVPNLSGAVQDAGLLVFTTPHKLIHKICNEITGRVPKKALRIIHTEGIDEGPGGLMLSSDIIRE

Parental  KMGIDISVLMGANIASEVAAEKFCETTIGSKVMQNGLLFKELLQTPNFRITVVDDADTVELCGALKNIVA
          K.G.D.SVLMGAN....VAA..FCETTIGSKV.QNG.LFKELLQTPNF.ITVVDDAD.VELCGALK.IVA
Retrocopy KIGMDVSVLMGANTVRVVAAGEFCETTIGSKVIQNGILFKELLQTPNFCITVVDDADDVELCGALKHIVA

Parental  VGAGFCDGLRCGDNTKAAVIRLGLMEMIAFAKIFCKGQVSTATFLESCGVADLITTCYGGRNRRVAEAFA
          .G..FCDGL.CG.N.KAA...LGL.E...F..IFCK.QVS.ATFLESCG.A.LITTCY.G....VA..F.
Retrocopy MGTTFCDGLHCGNNGKAAITHLGLVELVTFTRIFCKSQVSMATFLESCGLANLITTCYRGND*KVAKTFL

Parental  RTGKTIEELEKELLNGQKLQGPQTSAEVYRILRQKGLLDKFPLFTAVYQICYEGRPVTQMLSCLQSHPEH
          .TG.TI..LEKE.LNGQ.LQG...SA.VY..L.QKGLL.KFP.F..VY.ICYEG.P.T..L.CL.SHP.H
Retrocopy KTGETIRKLEKEMLNGQALQGLEISALVYQFLKQKGLLAKFP*FITVYWICYEGKPLTEILTCLLSHPAH

Parental  I
          .
Retrocopy V

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	107.73 RPM
SRP007412_cerebellum	0.00 RPM	64.83 RPM
SRP007412_heart	0.00 RPM	63.60 RPM
SRP007412_kidney	0.00 RPM	57.88 RPM
SRP007412_liver	0.00 RPM	34.68 RPM
SRP007412_testis	0.41 RPM	6.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1348 was not detected

EST

No EST(s) were mapped for retro_mmus_1348 retrocopy.

TSS

No TSS is located nearby retro_mmus_1348 retrocopy 5' end.

Lab

retro_mmus_1348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1348 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2474

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348 , retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,