RetrogeneDB ID: retro_mmus_1928

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:68081642..68082787(+)
• Located in intron of: ENSMUSG00000034780

Retrocopy information

• Ensembl ID: ENSMUSG00000081257
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Actl6a
• Ensembl ID: ENSMUSG00000027671
• Aliases: Actl6a, 2810432C06Rik, AI851094, ARP4, Actl6, Baf53a, C79802
• Description: actin-like 6A [Source:MGI Symbol;Acc:MGI:1861453]

Sequence

>retro_mmus_1928
ATGAACGGCGGCGTGTATGGCGGAAATGAAGTTGGTGCTCTTGTTTTTAACACTGAATCGTATATAGTGAGGCCTGGCTA
TGCTGGCGAGGACTGCCCTAAGGTTGATTTCCCCACGGCTATCAGTGTGGTGCTGGAAAGAGATGACTGAAGCACAACGA
TGGAGACTGATGGTGAGAAAGGCAAGCAGGGTGGGCCCACCTACTACATAGACACCAGAGCCCTCCAAGTGCCCAGGGAG
AACATGGAGGCCATCTCACCATTCAAGAACAACATGGTTGAAGACTGGGATAGTTTCCAGACAATTTTGGATCATACATA
CAAGATGCATGTCAAATCTGAAGCCAGCCTGCATCTTGTTCTCATGTCGGAAGCACCATGGAACACCAGGGCAAAGAGAG
AGAAACTGACAGAGTTGATGTTTCAGCACTACAGCATCCCTGAATTCTTCCTTTGCAAAACTACAGTTTTGATGGCGTTT
GCTAATGGTCATTCTACTGGGCTGATTTTGGACAGTGGAGCTACCCACACCACTTCGATTCCAGTCCACGATGGCTATGT
CCTTCAAAAAGGCATTGTGAAATCCCCTCTTGCTGGAGTCTTCATTACCATGCAGTACAAAGAACTCTTCCAGGAAATGA
ACATAGAACTCATTCCTCCTTACATGATTGCATTAAAAGAGGCTGTTTGAGTAGGCTCTCCAGCCAACTGGAAAAGAAAA
GAGAACCTGCCCCAGGTTACAAAGTCTTGGCACAATTACATGTGCAACGGTGTCACTCAGGACTTTCAAGCTTCTGTCCT
TCAGGTATTAGACTCCACCTATGACAAACAAGTGGCTTCACAGATGCCAACTATTCACTACGAATTCCCCAATGGTTACA
GCTGTGGTTTTGGTGCAAAGAGGCTGAAAATTCCTGAAGGATTATTTGACCCTTCCAACTAAAGGGCTTGTCTGGGAACA
TGATGCTGGGAGTCAGTCACATGGTCACAACCAGTGTCGGGATGTGTGACATCAATATCAGACCAAGTCTCTATGGCAGT
GTGATCATAGCAGGAGGAAACAAGCTAATACAGAGTTTCACTGACAGGATAAATAGAGACCTTTCTCAGAAAACTTCACC
AAGTATGTAGTTGAAACTGATTGCA

Alignment

ORF - retro_mmus_1928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.9 %
• Parental protein coverage: 89.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGGVYGGDEVGALVFDIGSYTVRAGYAGEDCPKVDFPTAIGVVLERDDGSTMMEIDGDKGKQGGPTYYI
          M.GGVYGG.EVGALVF...SY.VR.GYAGEDCPKVDFPTAI.VVLERDD.ST.ME.DG.KGKQGGPTYYI
Retrocopy MNGGVYGGNEVGALVFNTESYIVRPGYAGEDCPKVDFPTAISVVLERDD*STTMETDGEKGKQGGPTYYI

Parental  DTNALRVPRENMEAISPLKNGMVEDWDSFQAILDHTYKMHVKSEASLHPVLMSEAPWNTRAKREKLTELM
          DT.AL.VPRENMEAISP.KN.MVEDWDSFQ.ILDHTYKMHVKSEASLH.VLMSEAPWNTRAKREKLTELM
Retrocopy DTRALQVPRENMEAISPFKNNMVEDWDSFQTILDHTYKMHVKSEASLHLVLMSEAPWNTRAKREKLTELM

Parental  FEHYSIPAFFLCKTAVLTAFANGRSTGLILDSGATHTTAIPVHDGYVLQQGIVKSPLAGDFITMQCRELF
          F.HYSIP.FFLCKT.VL.AFANG.STGLILDSGATHTT.IPVHDGYVLQ.GIVKSPLAG.FITMQ..ELF
Retrocopy FQHYSIPEFFLCKTTVLMAFANGHSTGLILDSGATHTTSIPVHDGYVLQKGIVKSPLAGVFITMQYKELF

Parental  QEMNIELIPPYMIASKEAVREGSPANWKRKEKLPQVTRSWHNYMCNCVIQDFQASVLQVSDSTYDEQVAA
          QEMNIELIPPYMIA.KEAV..GSPANWKRKE.LPQVT.SWHNYMCN.V.QDFQASVLQV.DSTYD.QVA.
Retrocopy QEMNIELIPPYMIALKEAV*VGSPANWKRKENLPQVTKSWHNYMCNGVTQDFQASVLQVLDSTYDKQVAS

Parental  QMPTVHYEFPNGYNCDFGAERLKIPEGLFDPSN-VKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSVI
          QMPT.HYEFPNGY.C.FGA.RLKIPEGLFDPSN..KGLSGN.MLGVSH.VTTSVGMCDI.IRP.LYGSVI
Retrocopy QMPTIHYEFPNGYSCGFGAKRLKIPEGLFDPSN<LKGLSGNMMLGVSHMVTTSVGMCDINIRPSLYGSVI

Parental  VAGGNTLIQSFTDRLNRELSQKTPPSMRLKLIA
          .AGGN.LIQSFTDR.NR.LSQKT.PSM.LKLIA
Retrocopy IAGGNKLIQSFTDRINRDLSQKTSPSM*LKLIA

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	0.07 RPM	7.76 RPM
SRP007412_cerebellum	0.04 RPM	11.25 RPM
SRP007412_heart	0.00 RPM	19.92 RPM
SRP007412_kidney	0.00 RPM	23.83 RPM
SRP007412_liver	0.08 RPM	14.26 RPM
SRP007412_testis	0.00 RPM	92.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1928 was not detected

EST

No EST(s) were mapped for retro_mmus_1928 retrocopy.

TSS

No TSS is located nearby retro_mmus_1928 retrocopy 5' end.

Lab

retro_mmus_1928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1928 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009477	2 retrocopies	retro_chof_1481, retro_chof_909,
Mus musculus	ENSMUSG00000027671	1 retrocopy	retro_mmus_1928 ,
Tursiops truncatus	ENSTTRG00000008907	1 retrocopy	retro_ttru_1431,