RetrogeneDB ID: retro_mmus_2533

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:147735479..147738539(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081179
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Smarca5
• Ensembl ID: ENSMUSG00000031715
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 [Source:MGI Symbol;Acc:MGI:1935129]

Sequence

>retro_mmus_2533
CCGGCGGGAGCAGCAGCGGCAACAAAGGCGGCCCCGAGGGCTGCGGGCTCGTGCCCCGGCCCCGCGGACACCGAGATGGA
GGAAGTATTTGATAATGGATCACCTGGAAAGCAAAAAGAAATCCAAGAACCAGATCCTACATATGAAGAAAAAATGCAAA
CTGACCGAGCAAATAGATTTGAGTATTTATTAAAGCAGACAGAGCTGTTCGCTCATTTCATTCAGCCTGCTGCTCAGAAG
ACTCCAACCTCACCCTTGAAGATGAAACCAGGGCGCCCACGGGTAAAAAGGATGAAAAACAGAATTTGCTTTCAGTTGGA
GATTACCGACACTGTAGAACAGAGCAAGAGGAGGATGAAGAGCTATTAACAGAAAGTTCCAAAGCAACTAATGTTTGTAC
TCGATTTGAAGATTCTCCATCATATGTAAAATGGGGTAAACTGAGAGATTATCAGGTGCGAGGATTGAATTGGCTCATCT
CTCTGTATGAGAATGGCATCAATGGGATCCTTGCAGATGAAATGGGTTTGGGAAAGACACTTCAAACAATTTCTCTTCTT
GGATACAGGAAACACTATAGAAATATTCCTGGTCCTCATATGGTTTTGGTTCCCAAGTCTACATTGCACAACTGGATGAG
TGAATTCAAGAGATGGATACCAACACTTAGGTCTGTTTGCTTGATAGGAGATGAAGAGCAAAGAGCTGTATTTGTCAGGG
ATGTTTTATTACCAGGAGAGTGGGATGTGTGTGTCACATCTTATGAAATGCTTATTAAAGAGAAAGTCTGTGTTCAAAAA
AATTCAACTGGAGATACTTAGTTATAGATGAAGCTCACAGGATAAAAAATGAAAAAATCTAAGTTGTCAGAAACAGTGAG
AGAATTCAAGACTACAAATCGGCTGTTGCTAACAGGGACGCCTCTTCAGAACAACCTGCATGAGCTCTGGTCACTTCTAA
ACTTTTTGTTTCCAAATGTGTTTAATTCAGCTGATGACTTTGATTCCTGGGTTGATACAAATAATTGCCTTGGGGATCAA
AAGCTAGTTGAGAGGCTTCATATGGTTTTGTGTCCATTCCTCTTTCGTCGAATTAAAGCTGATGTTGAAAAGAGTTTGCC
TCCAAAAAAAGAAGTAAAAATCTATGTGGGTCTTAGCAAAATGCAAAGAGAATGGTATACTCGGATATTAATAAAAGATA
TAGACATATTAAACTCAGCAGGGAAGATGGACAAAATGAGGCTATTGAACATTTTGATGCAGTTGAGGAAATGCTGCAAT
CATCCGTATCTCTTCGATGGAGCTGAACCTGGTCCACTGTACACAACAGATACGCATCTTGTTACCAACAGTGGCAAGAT
GGTGGTGTTAGACAAGCTACTCCCTAAACTGAAAGAACAAGGTTCAAGAGTACTAATCTTTAGTCAGATGACAAGAGTAT
TAGACATTTTGGAAGATTATTGCATGTGGAGAAATTATGAGTACTGCAGGTTGGATGAACAGACACCCCATGATGAGAGA
CAAGACTCCATCAATGCATACAATGAACCAAATAGCACAAAGTTTGTATTTATGCTAAACACACGTGCTGGTGGTCTGGG
CATCAATCTTGCAACTGCTGATGTAGTAATTTTATATGATTCAGATTGGAATCCTCAAATTGATCTTCAGCCTATGGACC
ATGCCCATAGAATTGGACAAAGGAAGACTGTCCGAGTGTTTCGCTTTATAACTGATAACACTGTGGAAGAAAGAATAGTG
GAACGTGCTGAGATGAAACTTAGACTGGATTCGATAGTAATTCAACAAGGGAGGCTTGTAGATCAGAACCTGAACAAAAT
TGGGAAAGATGAAATGCTTCAAATGATTCGACGTGGTGCCACACATGTGTTTGCTTCAAAAGAAAGTGAAATCACTGATG
AGGATATTGATGGTATTTTAGAAAGAGGTGCAAAGAAGACTGCAGAAATGAATGAAAAGCTCTCCAAGATGGGTGAACGT
TCACTTAGAAACTTTACGATGGATACAGAGTCCAGTGTTTATAACTTTGAAGGAGAAGACTATAGAGAAAAACAAAAGAG
TGCATTCACAGAGTGGATTGAACCACCAAAAAGAGAAAGAAAAGCCAACTATGCTGTTGATGCATATTTCAGGGAAGCTC
TCCGTGTTAGTGAGCCTAAAGCACCCAAGGCACCTCGACCTCCAAAACAACTAAATGTTCAGGATTTCCAGTTCTTTCCT
CCAGGTTTATGTGAATTACTGGAAAAAGAAATTCTGTATTACAGGAAAACTATTGGGTATAAGGTACCTTGGAGTCCTGA
TCTACCTAATGCAGCACAGGCATAGAAAGAACAGCTAAAAATTGATGAAGCAGAGACCCTCAATGACGAGGAGTTAGAGG
AAAAAGAGAAGCTTCTGACACAGGGGTTTACAAATTGGAATAAGAGAGATTTTAACCAGTTTATCAAGGCTAATGAGAAG
TGGGGTCGTGATGATATTGAAAATATAGCCAGAGAATTAGAAGGAAAAACTCCAGAAGAAGTCATTGAATACTCAGCTGT
GTTCTGGGAAAGATGCAATGAGCTTCAGGACATAGAGAAGATTATGGCTCAGATTGAAAGGGGAGAGGCAAGAATTCAAA
GAAGAATAAGTATCAAGAAAGCACTAGATACAAAGATTGGACGGTACAAAGCACACTTTCATCAGCTAAGAATATCATAT
GGTACTAACAAAGGAAAAAAACTATACTGAAGAAGAGGATCGTTTTCTCATTTGTATGCTGCACAAGCTTGGCTTCGACA
AGGAAAATGTGTATGATGAATTACGACAATGCATCCGAAACTCCCCTCAGTTTAGATTTGATTGGTTTCTCAAGTCCAGA
ACTGCGATGGCGCTCCAGAGGAGGTGTAATACCTTAATTACTTTGATTGAAAGAGAAAGTATGGAACTAGAAGAAAAGGA
GAAGGCAGAGAAAAAGAAAAGAGGACCAAAACCTTCCACACAGAAACATAAGATGGACGGTGCCCTTGATGGCCGTGGAA
GAAAAAAGAAGCTGAAACTA

Alignment

ORF - retro_mmus_2533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.54 %
• Parental protein coverage: 96.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PEGGAAP--AAPCAAGS--GPADTEMEEVFDHGSPGKQKEIQEPDPTYEEKMQTDRANRFEYLLKQTELF
          P.G.AA...AAP.AAGS..GPADTEMEEVFD.GSPGKQKEIQEPDPTYEEKMQTDRANRFEYLLKQTELF
Retrocopy PAGAAAATKAAPRAAGSCPGPADTEMEEVFDNGSPGKQKEIQEPDPTYEEKMQTDRANRFEYLLKQTELF

Parental  AHFIQPAAQKTPTSPLKMKPGRPRVK-KDEKQNLLSVGDYRHRRTEQEEDEELLTESSKATNVCTRFEDS
          AHFIQPAAQKTPTSPLKMKPGRPRVK.KDEKQNLLSVGDYRH.RTEQEEDEELLTESSKATNVCTRFEDS
Retrocopy AHFIQPAAQKTPTSPLKMKPGRPRVK<KDEKQNLLSVGDYRHCRTEQEEDEELLTESSKATNVCTRFEDS

Parental  PSYVKWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIPGPHMVLVPKSTL
          PSYVKWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGY.KHYRNIPGPHMVLVPKSTL
Retrocopy PSYVKWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYRKHYRNIPGPHMVLVPKSTL

Parental  HNWMSEFKKWVPTLRSVCLIGDKEQRAAFVRDVLLPGEWDVCVTSYEMLIKEK-SVFKK-FNWRYLVIDE
          HNWMSEFK.W.PTLRSVCLIGD.EQRA.FVRDVLLPGEWDVCVTSYEMLIKEK.SVFKK.FNWRYLVIDE
Retrocopy HNWMSEFKRWIPTLRSVCLIGDEEQRAVFVRDVLLPGEWDVCVTSYEMLIKEK>SVFKK>FNWRYLVIDE

Parental  AHRIKNEK-SKLSEIVREFKTTNRLLLTGTPLQNNLHELWSLLNFLLPDVFNSADDFDSWFDTNNCLGDQ
          AHR......SKLSE.VREFKTTNRLLLTGTPLQNNLHELWSLLNFL.P.VFNSADDFDSW.DTNNCLGDQ
Retrocopy AHRXXXXX>SKLSETVREFKTTNRLLLTGTPLQNNLHELWSLLNFLFPNVFNSADDFDSWVDTNNCLGDQ

Parental  KLVERLHMVLRPFLLRRIKADVEKSLPPKKEVKIYVGLSKMQREWYTRILMKDIDILNSAGKMDKMRLLN
          KLVERLHMVL.PFL.RRIKADVEKSLPPKKEVKIYVGLSKMQREWYTRIL.KDIDILNSAGKMDKMRLLN
Retrocopy KLVERLHMVLCPFLFRRIKADVEKSLPPKKEVKIYVGLSKMQREWYTRILIKDIDILNSAGKMDKMRLLN

Parental  ILMQLRKCCNHPYLFDGAEPGPPYTTDMHLVTNSGKMVVLDKLLPKLKEQGSRVLIFSQMTRVLDILEDY
          ILMQLRKCCNHPYLFDGAEPGP.YTTD.HLVTNSGKMVVLDKLLPKLKEQGSRVLIFSQMTRVLDILEDY
Retrocopy ILMQLRKCCNHPYLFDGAEPGPLYTTDTHLVTNSGKMVVLDKLLPKLKEQGSRVLIFSQMTRVLDILEDY

Parental  CMWRNYEYCRLDGQTPHDERQDSINAYNEPNSTKFVFMLSTRAGGLGINLATADVVILYDSDWNPQVDLQ
          CMWRNYEYCRLD.QTPHDERQDSINAYNEPNSTKFVFML.TRAGGLGINLATADVVILYDSDWNPQ.DLQ
Retrocopy CMWRNYEYCRLDEQTPHDERQDSINAYNEPNSTKFVFMLNTRAGGLGINLATADVVILYDSDWNPQIDLQ

Parental  AMDRAHRIGQTKTVRVFRFITDNTVEERIVERAEMKLRLDSIVIQQGRLVDQNLNKIGKDEMLQMIRHGA
          .MD.AHRIGQ.KTVRVFRFITDNTVEERIVERAEMKLRLDSIVIQQGRLVDQNLNKIGKDEMLQMIR.GA
Retrocopy PMDHAHRIGQRKTVRVFRFITDNTVEERIVERAEMKLRLDSIVIQQGRLVDQNLNKIGKDEMLQMIRRGA

Parental  THVFASKESEITDEDIDGILERGAKKTAEMNEKLSKMGESSLRNFTMDTESSVYNFEGEDYREKQKIAFT
          THVFASKESEITDEDIDGILERGAKKTAEMNEKLSKMGE.SLRNFTMDTESSVYNFEGEDYREKQK.AFT
Retrocopy THVFASKESEITDEDIDGILERGAKKTAEMNEKLSKMGERSLRNFTMDTESSVYNFEGEDYREKQKSAFT

Parental  EWIEPPKRERKANYAVDAYFREALRVSEPKAPKAPRPPKQPNVQDFQFFPPRLFELLEKEILYYRKTIGY
          EWIEPPKRERKANYAVDAYFREALRVSEPKAPKAPRPPKQ.NVQDFQFFPP.L.ELLEKEILYYRKTIGY
Retrocopy EWIEPPKRERKANYAVDAYFREALRVSEPKAPKAPRPPKQLNVQDFQFFPPGLCELLEKEILYYRKTIGY

Parental  KVPRSPDLPNAAQAQKEEQLKIDEAEPLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENI
          KVP.SPDLPNAAQA.K.EQLKIDEAE.LNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENI
Retrocopy KVPWSPDLPNAAQA*K-EQLKIDEAETLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENI

Parental  AREVEGKTPEEVIEYSAVFWERCNELQDIEKIMAQIERGEARIQRRISIKKALDTKIGRYKAPFHQLRIS
          ARE.EGKTPEEVIEYSAVFWERCNELQDIEKIMAQIERGEARIQRRISIKKALDTKIGRYKA.FHQLRIS
Retrocopy ARELEGKTPEEVIEYSAVFWERCNELQDIEKIMAQIERGEARIQRRISIKKALDTKIGRYKAHFHQLRIS

Parental  YGTNKG-KNYTEEEDRFLICMLHKLGFDKENVYDELRQCIRNSPQFRFDWFLKSRTAMELQRRCNTLITL
          YGTNKG.KNYTEEEDRFLICMLHKLGFDKENVYDELRQCIRNSPQFRFDWFLKSRTAM.LQRRCNTLITL
Retrocopy YGTNKG>KNYTEEEDRFLICMLHKLGFDKENVYDELRQCIRNSPQFRFDWFLKSRTAMALQRRCNTLITL

Parental  IERENMELEEKEKAEKKKRGPKPSTQKRKMDGAPDGRGRKKKLKL
          IERE.MELEEKEKAEKKKRGPKPSTQK.KMDGA.DGRGRKKKLKL
Retrocopy IERESMELEEKEKAEKKKRGPKPSTQKHKMDGALDGRGRKKKLKL

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	40.79 RPM
SRP007412_cerebellum	0.00 RPM	35.21 RPM
SRP007412_heart	0.00 RPM	25.40 RPM
SRP007412_kidney	0.02 RPM	33.40 RPM
SRP007412_liver	0.00 RPM	24.50 RPM
SRP007412_testis	0.82 RPM	69.43 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2533 was not detected

EST

No EST(s) were mapped for retro_mmus_2533 retrocopy.

TSS

No TSS is located nearby retro_mmus_2533 retrocopy 5' end.

Lab

retro_mmus_2533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2533 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000031715	5 retrocopies	retro_mmus_2406, retro_mmus_2413, retro_mmus_2419, retro_mmus_2424, retro_mmus_2533 ,