RetrogeneDB ID: retro_mmus_353

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:112137865..112138702(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hax1
• Ensembl ID: ENSMUSG00000027944
• Aliases: Hax1, HAX-1, HSP1BP-1, Hs1bp1, SIG-111, Silg111, mHAX-1s
• Description: HCLS1 associated X-1 [Source:MGI Symbol;Acc:MGI:1346319]

Sequence

>retro_mmus_353
ATGAGTGTCTTTGATCTTTTCCGAGGCTGTTTCAGCTTTCTTGGACCTCAGAGCCCCAGAGATCCTTTTTATGGAGGATG
ACTCGAGATTATGATGAAGATAATGATGATAATGATGAAGTGGAAGAAGACAGAGGCATGTGGGGTCGAGAGAGCTATGT
GTTTGATGGTTCTCAGCCTCCAGAGTAATTTGATTTTAGCTTTAGCCCCAGAGGAGGGATGCGATTCCATGGCAACTTTG
ACTTTGATGATCTAGTACGAGATTTTAATAGCATCTTCAGCGAGATGGAGGCCTGGACCTTGCCTTCCCACTTTCCTGAA
CTTTCAGGTCTTGAGTCAGAAACACCTGGTGAGAGACTGCAGGAGGGGCAGACACTATGAGACTCAATGCTTAAGTACCC
AGATAGTCACCAACCCAGGATCTTTGAGAGGGTCTTAGAGAGTCATGCAAAGCCTGAATCCCCCAAACCAGCTCCAGATT
GGGGGGTCCTAGGGATCTTTTCATAGGTTGGATGATACATGACTTGTGAGTCCCCATTCTAGAGCCATAGAAGACAAAGA
TCTTGACTCCCGGGTTTCCCAGGAAGGTCTGGATCCACTTCTTCAATCCCAGCCCAAATCGTATTTCAAAAGCATCTCTG
TGACCAAGATTACTAAGCCAGATGGGACAGTGGAGGAACACCACACTTTGGTAGACAGTGAGGGCCTGAGAGAGACCACA
GTGATTCATCAAGAAACCCGTGCAGGTTCCAGAAGTGATCCAGACTCTCAGAGATCTTCAACTTTGGCTGATCCCCTTTC
CATTCTGGATTTGCTCCTAGGCCCTTGGTTTAGGTCC

Alignment

ORF - retro_mmus_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.49 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVFDLFRGFFGFPGPRSHRDPFFGG-MTRDDDDDDDDDDEAEEDRGAWGRESYAFDGSQPPEEFGFSFS
          MSVFDLFRG.F.F.GP.S.RDPF.GG.MTRD...........EEDRG.WGRESY.FDGSQPPE.F.FSFS
Retrocopy MSVFDLFRGCFSFLGPQSPRDPFYGG<MTRDYXXXXXXXXXVEEDRGMWGRESYVFDGSQPPE*FDFSFS

Parental  PRGGMRFHGNFGFDDLVRDFNSIFSEMGAWTLPSHSPELPGPESETPGERLREGQTLRDSMLKYPDSHQP
          PRGGMRFHGNF.FDDLVRDFNSIFSEM.AWTLPSH.PEL.G.ESETPGERL.EGQTL.DSMLKYPDSHQP
Retrocopy PRGGMRFHGNFDFDDLVRDFNSIFSEMEAWTLPSHFPELSGLESETPGERLQEGQTL*DSMLKYPDSHQP

Parental  RIFEGVLESHAKPESPKPAPDWG-SQGPFHRLDDTWPVSPHSRAKEDKDLDSQVSQEGLGPLLQPQPKSY
          RIFE.VLESHAKPESPKPAPDWG.S.G.FHRLDDT..VSPHSRA.EDKDLDS.VSQEGL.PLLQ.QPKSY
Retrocopy RIFERVLESHAKPESPKPAPDWG>S*GSFHRLDDT*LVSPHSRAIEDKDLDSRVSQEGLDPLLQSQPKSY

Parental  FKSISVTKITKPDGTVEERRTVVDSEGRRETTVTHQEAHDSSRSDPDSQRSSALDDPFSILDLLLGRWFR
          FKSISVTKITKPDGTVEE..T.VDSEG.RETTV.HQE....SRSDPDSQRSS.L.DP.SILDLLLG.WFR
Retrocopy FKSISVTKITKPDGTVEEHHTLVDSEGLRETTVIHQETRAGSRSDPDSQRSSTLADPLSILDLLLGPWFR

Parental  S
          S
Retrocopy S

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	12.08 RPM
SRP007412_cerebellum	0.00 RPM	15.68 RPM
SRP007412_heart	0.03 RPM	10.09 RPM
SRP007412_kidney	0.00 RPM	31.34 RPM
SRP007412_liver	0.00 RPM	25.31 RPM
SRP007412_testis	0.00 RPM	41.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_353 was not detected

EST

No EST(s) were mapped for retro_mmus_353 retrocopy.

TSS

No TSS is located nearby retro_mmus_353 retrocopy 5' end.

Lab

retro_mmus_353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_353 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
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353 ,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,