RetrogeneDB ID: retro_mmus_205

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:186967875..186969858(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000039224
• Aliases: D1Pas1, Pl10
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ddx3x
• Ensembl ID: ENSMUSG00000000787
• Aliases: Ddx3x, D1Pas1-rs2, Ddx3, Fin14
• Description: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked [Source:MGI Symbol;Acc:MGI:103064]

Sequence

>retro_mmus_205
ATGAGTCATGTGGCAGAGGAAGATGAGCTCGGGCTGGACCAGCAGTTGGCTGGCCTAGACCTGACGTCTCGGGACAGCCA
GAGCGGGGGCAGCACAGCCAGCAAAGGGCGCTACATCCCCCCTCACCTGCGGAACCGGGAGGCCGCGAAGGCGTTCTACG
ACAAAGACGGCTCACGGTGGAGTAAAGACAAGGATGCCTACAGCAGCTTCGGGTCCCGCAGCGACACGAGAGCCAAGTCC
AGTTTCTTCAGTGACCGCGGCGGAAGCGGCTCCAGGGGAAGGTTTGACGAGCGCGGGCGGAGTGACTACGAGAGTGTTGG
CAGCCGGGGAGGTAGAAGTGGCTTTGGCAAATTTGAGCGGGGCGGGAACAGTCGCTGGTGTGACAAAGCAGACGAGGATG
ACTGGTCGAAACCGCTCCCACCAAGCGAACGCTTGGAACAGGAACTCTTTTCCGGAGGCAACACTGGGATTAACTTTGAG
AAATATGATGACATCCCGGTTGAGGCGACAGGGAATAACTGCCCTCCACATATTGAAAGTTTCAGCGATGTCGAGATGGG
AGAGATTATTATGGGAAACATCGAGCTCACTCGTTACACACGCCCAACTCCTGTGCAAAAGCATGCTATTCCTATTATCA
AGGAGAAAAGAGACTTGATGGCTTGTGCCCAAACGGGGTCTGGAAAAACAGCAGCTTTTCTTCTACCTATCTTGAGTCAG
ATCTATACGGATGGTCCAGGTGAGGCTTTGAGGGCCATGAAGGAGAATGGAAAGTATGGGCGTCGCAAACAGTATCCAAT
CTCCTTGGTCTTGGCTCCGACCAGAGAATTGGCCGTGCAGATCTATGAGGAGGCCAGGAAATTCTCATACCGCTCTCGAG
TTCGTCCTTGTGTGGTTTATGGTGGAGCTGATATTGGGCAGCAGATTCGAGACTTGGAACGTGGCTGTCACTTGTTAGTA
GCTACTCCAGGACGGCTAGTAGATATGATGGAGAGAGGAAAGATTGGACTGGACTTCTGCAAATACTTGGTGTTAGATGA
AGCAGATCGAATGTTGGACATGGGCTTTGAGCCTCAGATACGAAGAATAGTTGAGCAAGACACCATGCCTCCAAAAGGTG
TCCGCCACACTATGATGTTTAGTGCTACCTTTCCTAAGGAAATACAGATGCTGGCTCGGGATTTCTTGGATGAATATATC
TTTCTGGCCGTAGGAAGAGTTGGGTCTACTTCTGAGAACATCACACAGAAAGTCGTGTGGGTGGAAGAAGCAGACAAGCG
GTCATTTCTGCTTGACCTCCTGAATGCAACGGGCAAGGATTCCCTGATATTGGTGTTTGTGGAAACCAAAAAGGGTGCAG
ATTCTCTGGAGGACTTCTTATACCACGAAGGATATGCTTGTACCAGTATCCATGGAGACCGATCTCAGCGAGATAGGGAA
GAGGCCCTTCACCAATTCCGATCAGGAAAAAGCCCAATTCTCGTGGCTACAGCAGTAGCTGCAAGAGGACTGGATATTTC
CAATGTGAAACATGTCATCAATTTCGACTTGCCTAGTGACATCGAAGAATATGTGCATCGCATTGGCCGTACAGGTCGTG
TTGGAAACCTTGGCCTTGCCACCTCATTCTTCAACGAGAGGAACATAAATATTACCAAAGATTTATTGGATCTTCTTGTT
GAAGCAAAACAAGAAGTGCCATCTTGGCTAGAAAACATGGCTTTTGAACACCATTACAAGGGTGGCAGTCGTGGACGGTC
CAAGAGCAGATTTAGTGGAGGATTTGGTGCTAGAGACTATCGACAAAGTAGCGGTGCCAGCAGTTCCAGCTTCAGCAGTG
GCCGTGCTAGCAACAGTCGCAGCGGTGGAGGCAGCCATGGCAGCAGCAGAGGGTTTGGTGGAGGTAGCTATGGAGGCTTT
TACAACAGTGATGGATATGGAGGAAATTATAGCTCCCAGGGGGTTGACTGGTGGGGTAACTGA

Alignment

ORF - retro_mmus_205 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHVAVENALGLDQQFAGLDLNSSDNQSGGSTASKGRYIPPHLRNREATKGFYDKDSSGWSSSKDKDAYS
          MSHVA.E..LGLDQQ.AGLDL.S.D.QSGGSTASKGRYIPPHLRNREA.K.FYDKD.S.WS..KDKDAYS
Retrocopy MSHVAEEDELGLDQQLAGLDLTSRDSQSGGSTASKGRYIPPHLRNREAAKAFYDKDGSRWS--KDKDAYS

Parental  SFGSRGDSRGKSSFFGDRG-SGSRGRFDDRGRGDYDGIGGRGDRSGFGKFERGGNSRWCDKSDEDDWSKP
          SFGSR.D.R.KSSFF.DRG.SGSRGRFD.RGR.DY...G.RG.RSGFGKFERGGNSRWCDK.DEDDWSKP
Retrocopy SFGSRSDTRAKSSFFSDRGGSGSRGRFDERGRSDYESVGSRGGRSGFGKFERGGNSRWCDKADEDDWSKP

Parental  LPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKH
          LPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKH
Retrocopy LPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKH

Parental  AIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYADGPGEALRAMKENGRYGRRKQYPISLVLAPTRELA
          AIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIY.DGPGEALRAMKENG.YGRRKQYPISLVLAPTRELA
Retrocopy AIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYTDGPGEALRAMKENGKYGRRKQYPISLVLAPTRELA

Parental  VQIYEEARKFSYRSRVRPCVVYGGAEIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEA
          VQIYEEARKFSYRSRVRPCVVYGGA.IGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEA
Retrocopy VQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEA

Parental  DRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKV
          DRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKV
Retrocopy DRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKV

Parental  VWVEEIDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRS
          VWVEE.DKRSFLLDLLNATGKDSL.LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRS
Retrocopy VWVEEADKRSFLLDLLNATGKDSLILVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRS

Parental  GKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDL
          GKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDL
Retrocopy GKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDL

Parental  LVEAKQEVPSWLENMAFEHHYKGSSRGRSKSSRFSGGFGARDYRQSSGASSSSFSSSRASSSRSGGGGHG
          LVEAKQEVPSWLENMAFEHHYKG.SRGRSK.SRFSGGFGARDYRQSSGASSSSFSS.RAS.SRSGGG.HG
Retrocopy LVEAKQEVPSWLENMAFEHHYKGGSRGRSK-SRFSGGFGARDYRQSSGASSSSFSSGRASNSRSGGGSHG

Parental  GSRGFGGGGYGGFYNSDGYGGNYNSQGVDWWGN
          .SRGFGGG.YGGFYNSDGYGGNY.SQGVDWWGN
Retrocopy SSRGFGGGSYGGFYNSDGYGGNYSSQGVDWWGN

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	0.05 RPM	210.69 RPM
SRP007412_cerebellum	0.09 RPM	222.97 RPM
SRP007412_heart	0.06 RPM	218.81 RPM
SRP007412_kidney	0.00 RPM	285.76 RPM
SRP007412_liver	0.08 RPM	248.10 RPM
SRP007412_testis	254.77 RPM	34.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_205 was not detected

EST

No EST(s) were mapped for retro_mmus_205 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_73153	1019 libraries	43 libraries	8 libraries	2 libraries	0 libraries
TSS #2	TSS_73154	1000 libraries	36 libraries	15 libraries	13 libraries	8 libraries

The graphical summary, for retro_mmus_205 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_205 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_205 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035907	1 retrocopy	retro_btau_1846,
Callithrix jacchus	ENSCJAG00000009050	2 retrocopies	retro_cjac_1428, retro_cjac_4062,
Cavia porcellus	ENSCPOG00000013557	2 retrocopies	retro_cpor_326, retro_cpor_53,
Equus caballus	ENSECAG00000009901	1 retrocopy	retro_ecab_413,
Homo sapiens	ENSG00000215301	1 retrocopy	retro_hsap_4709,
Macaca mulatta	ENSMMUG00000017569	2 retrocopies	retro_mmul_1898, retro_mmul_2504,
Mus musculus	ENSMUSG00000000787	1 retrocopy	retro_mmus_205 ,
Ornithorhynchus anatinus	ENSOANG00000011274	1 retrocopy	retro_oana_64,
Pongo abelii	ENSPPYG00000020257	1 retrocopy	retro_pabe_3657,
Pan troglodytes	ENSPTRG00000022488	1 retrocopy	retro_ptro_3130,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415,