RetrogeneDB ID: retro_mmus_3475

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:75915490..75916523(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083544
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Oat
• Ensembl ID: ENSMUSG00000030934
• Aliases: Oat, AI194874
• Description: ornithine aminotransferase [Source:MGI Symbol;Acc:MGI:97394]

Sequence

>retro_mmus_3475
AAGATCATAGATGCTGTGAAGAGTCAGGTGGACAAGTCAACATTAATATCTCAGGCTTTCTATAACTATGTCCTTGGTGA
ATACAAGCAGTACATCACCAAGCTTTTCAACTACAACAAAGTTCTTCCTATGAATACAGGAGTGGAGGCTGGAGAGACTG
AATGTAAGCTTTCTTGTCCTTGGGCTACACAGTGAAAGGCATCCAGAAATACAAAGCAAAGATTTTTTTTTTCTGTTGGA
AACGTTTGGGGTTGAAAGTTGTGAGCAGTCTCCAGTTCTGCAGATCCGTCCAGTTACAATGGCTTTGGATTCTTCCTGCC
AGGCTTTGAAACCATCCCGTTTAAGGATCTGCCTACACTGGAGCATGCTCTTCAGGATCCAAATGTTGCTGCTTTCATGG
TGGGGCCCATCCAGGGTGAAGCAGGTGTTATTGTTCTGGATCCAAGACACCTGACCAGAGTTTGAGAACTCTGTACCAGG
CACCAGGTTCTGTTTATTGCTGATGAAATACAGACAGGATTGGCCAAAACTGGTAGATGGCTAGCTGTGGATCATAAAAA
TTTCAGACCTGACATAGTTCTTCTTGGGAAGGCCCTTTCTGATGGCTTATACCCTTTGTCTGCAGTCCTGTGTGATGATG
ACATAACGCTGACCAATAAGACAGGCGAGCATGGCTCTACATACGGCAGCAACCCACTAGGCAGCCAAATTGCCATTGTG
GTTCTTGAGGTTTTAGAAGAAGATAATCTTGCTGAAAATGCAGACAAGATAGGTGCTATCTTGAGAAAGGAGCTCACGAA
GCTGCCCTCTGACCTTGTGACTGCTGTGAGAGAGAAAGGGTTGCTAAATGCCATTGTCATCAGAGAAAACAAAGATTGTG
ATACTTGGATGGTTGTGCCTGCAACTCTGAGATAATGGGCTTCTGGCCAAGCCAACTCACTGCGATATCATCAGGTTTGC
CTCTCCACTTGTGATCAAGGAAGATGAGATCCAGGAGTCAGTGGAGATCATCAACAAGGCCGTCTTGTTCTTC

Alignment

ORF - retro_mmus_3475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.96 %
• Parental protein coverage: 78.36 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KIIDAMKSQVDKLTLTSRAFYNNVLGEYEEYITKLFNYNKVLPMNTGVEAGETACKLARRW-GYTVKGIQ
          KIIDA.KSQVDK.TL.S.AFYN.VLGEY..YITKLFNYNKVLPMNTGVEAGET.CKL...W.GYTVKGIQ
Retrocopy KIIDAVKSQVDKSTLISQAFYNYVLGEYKQYITKLFNYNKVLPMNTGVEAGETECKLSCPW<GYTVKGIQ

Parental  KYKA-KIVFADGNFWGRTLSAISSSTDPTSYDGFGPFMPGFETIPYNDLPALERALQDPNVAAFMVEPIQ
          KYKA.......GN.WG..L.A.SSS.DP.SY.GFG.F.PGFETIP..DLP.LE.ALQDPNVAAFMV.PIQ
Retrocopy KYKA>RXXXXVGNVWG*KL*AVSSSADPSSYNGFGFFLPGFETIPFKDLPTLEHALQDPNVAAFMVGPIQ

Parental  GEAGVIVPDPGYLTGVRELCTRHQVLFIADEIQTGLARTGRWLAVDHENVRPDMVLLGKALSGGLYPVSA
          GEAGVIV.DP..LT.V.ELCTRHQVLFIADEIQTGLA.TGRWLAVDH.N.RPD.VLLGKALS.GLYP.SA
Retrocopy GEAGVIVLDPRHLTRV*ELCTRHQVLFIADEIQTGLAKTGRWLAVDHKNFRPDIVLLGKALSDGLYPLSA

Parental  VLCDDEIMLTIKPGEHGSTYGGNPLGCRIAIAALEVLEEENLAENADKMGAILRKELMKLPSDVVTSVRG
          VLCDD.I.LT.K.GEHGSTYG.NPLG..IAI..LEVLEE.NLAENADK.GAILRKEL.KLPSD.VT.VR.
Retrocopy VLCDDDITLTNKTGEHGSTYGSNPLGSQIAIVVLEVLEEDNLAENADKIGAILRKELTKLPSDLVTAVRE

Parental  KGLLNAIVIRETKDCDAWKV-CLRLRDNGLLAKPTHGDIIRLAPPLVIKEDEIRESVEIINKTILSF
          KGLLNAIVIRE.KDCD.W.V.CL.L.DNGLLAKPTH.DIIR.A.PLVIKEDEI.ESVEIINK..L.F
Retrocopy KGLLNAIVIRENKDCDTWMV>CLQL*DNGLLAKPTHCDIIRFASPLVIKEDEIQESVEIINKAVLFF

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	67.03 RPM
SRP007412_cerebellum	0.00 RPM	62.35 RPM
SRP007412_heart	0.00 RPM	146.03 RPM
SRP007412_kidney	0.02 RPM	213.19 RPM
SRP007412_liver	0.05 RPM	678.15 RPM
SRP007412_testis	0.00 RPM	25.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3475 was not detected

EST

No EST(s) were mapped for retro_mmus_3475 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_158062	372 libraries	247 libraries	365 libraries	61 libraries	27 libraries

The graphical summary, for retro_mmus_3475 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3475 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012633	1 retrocopy	retro_cjac_2462,
Homo sapiens	ENSG00000065154	1 retrocopy	retro_hsap_4828,
Gorilla gorilla	ENSGGOG00000000848	1 retrocopy	retro_ggor_3010,
Macropus eugenii	ENSMEUG00000005655	1 retrocopy	retro_meug_613,
Mus musculus	ENSMUSG00000030934	1 retrocopy	retro_mmus_3475 ,
Nomascus leucogenys	ENSNLEG00000000482	2 retrocopies	retro_nleu_2176, retro_nleu_503,
Pongo abelii	ENSPPYG00000002737	2 retrocopies	retro_pabe_2989, retro_pabe_3754,
Pan troglodytes	ENSPTRG00000003028	1 retrocopy	retro_ptro_3213,
Sus scrofa	ENSSSCG00000010734	1 retrocopy	retro_sscr_1181,
Tursiops truncatus	ENSTTRG00000004225	1 retrocopy	retro_ttru_87,