RetrogeneDB ID: retro_mmus_2346

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:47453631..47454950(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081152
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mfap1b
• Ensembl ID: ENSMUSG00000048222
• Aliases: None
• Description: microfibrillar-associated protein 1B [Source:MGI Symbol;Acc:MGI:3694697]

Sequence

>retro_mmus_2346
ATGTCGGTCCTAAGCGCACTCACGAAGCAGCCGCCCATCCAGTCTACGGCTGGGGCCGTCCCAGTCCCAGTTCGCAAGGA
GAAAGGTGAGATCTCAATGGAAAAGGTGAAGGTGAAACGTTATGTGTCCGGAAAGAGACCAGATTATGCCCCTATGGAGT
CCTCAGATGAAGAGGATGAAGAATTTCAGTTCATTAAGAAAGCTAAGGGACAAGAAGCAGAGCCTGAGGAACAGGAGGAG
GACTCATCCAGTGACCCCCGACTTCGGAGGTTACAGAACCGCATCAGTGAAGATGTGGAAGAGCGATTGACTCGACACAG
AAAGATCGTGGAACCTGAAGTAGTGGGAGAGAGTGACTCAGAAGTAGAAGGGGATGCTTGGCGCCTGGAACGGGAAGATA
GCAGTAAGGAAGAGGAGGAAGAGATTGATGATGAAGAAATCGAGCGACGCCGAGGCATGATGCGTCAGCGAGCACAGGAG
AGGAAAAATGAAGAGATGGAAGTCATGGAGGTGGAAGATGAAGGGCGCTCTGGGGAGGAGTCTGAGTCAGAGTCTGAGTA
TGAGGAGTACACAGACAGTGAGGATGAAATGGAGCCTCGACTTAAGCCTGTCTTCATTCGAAAGAAGGATCCGGTGACAG
TTCAAGAACGAGAAGCTGAAGCATTGAAAGAGAAGGAACTGGAACAAGAAGCAAAATGCATGGCTGAGGAGCGGTGCAAG
TACACCCTCAAGATTGTAGAAGAAGAGACCAAGAAAGAGCTAGAGGAGAACATGCGGTCTCTTGCTGCCCTGGATGCGCT
CAATACTGATGATGAAAATGATGAGGAGTACGAGGTATGGAAAGTGCGCGAGCTCAAAAGAATCAAGCGGGAGAGAGAAG
ACCGAGAAGCGCTTGAAAAGGAGAAAGCAGAAATTGAACGCATGAGAAATCTGACTGAGGAAGAAAGGCGGGCAGAACTT
CGGGCAAATGGCAAAGTCATTACCAACAAAGCTGTTAAAGGCAAATACAAGTTTCTACAGAAGTATTGTCACCGAGGTGC
CTTCTTCATGGATGAGGATGAAGAAGTCTACAAGAGAGATTTTAGTGCACCACTCTTGAGGACCATTTCAATAAAACCAT
TCTTCCTAAAGTCATGCAGGTGAAGAATTTTGGACGGTCTGGTCGCACCAAGAACACCCACCTTGTGGATCAAGATACCA
ATTCCTTTGACTCTGCATGGGGCCAAGAGAGTACCCAGAACACAAAATTCTTTAAACAAAAGGCAGCAGGGGTACGAGAT
GTATTTGAGCAACCATCTGCCAAGAAGAGGAAAACCACC

Alignment

ORF - retro_mmus_2346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVPSALMKQPPIQSTAGAVPV--RNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAKE
          MSV.SAL.KQPPIQSTAGAVPV..R.EKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAK.
Retrocopy MSVLSALTKQPPIQSTAGAVPVPVRKEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAKG

Parental  QEAEPEEQEEDSSSDPRLRRLQNRISEDVEERLARHRKIVEPEVVGESDSEVEGDAWRLEREDSSEEEEE
          QEAEPEEQEEDSSSDPRLRRLQNRISEDVEERL.RHRKIVEPEVVGESDSEVEGDAWRLEREDSS.EEEE
Retrocopy QEAEPEEQEEDSSSDPRLRRLQNRISEDVEERLTRHRKIVEPEVVGESDSEVEGDAWRLEREDSSKEEEE

Parental  EIDDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEESESESEYEEYTDSEDEMEPRLKPVFIRKKD
          EIDDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGE.........EYTDSEDEMEPRLKPVFIRKKD
Retrocopy EIDDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEXXXXXXXXXEYTDSEDEMEPRLKPVFIRKKD

Parental  RVTVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEA
          .VTVQEREAEALK.KELEQEAK.MAEER.KYTLKIVEEETKKELEEN.RSLAALDALNTDDEND.EEYE.
Retrocopy PVTVQEREAEALKEKELEQEAKCMAEERCKYTLKIVEEETKKELEENMRSLAALDALNTDDEND-EEYEV

Parental  WKVRELKRIKREREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGAFF
          WKVRELKRIKREREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKY.HRGAFF
Retrocopy WKVRELKRIKREREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYCHRGAFF

Parental  MDEDEEVYKRDFSAP-TLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFF
          MDEDEEVYKRDFSAP.TLEDHFNKTILPKVMQVKNFGRSGRTK.THLVDQDT.SFDSAWGQES.QNTKFF
Retrocopy MDEDEEVYKRDFSAP<TLEDHFNKTILPKVMQVKNFGRSGRTKNTHLVDQDTNSFDSAWGQESTQNTKFF

Parental  KQKAAGVRDVFERPSAKKRKTT
          KQKAAGVRDVFE.PSAKKRKTT
Retrocopy KQKAAGVRDVFEQPSAKKRKTT

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	0.02 RPM	9.39 RPM
SRP007412_cerebellum	0.22 RPM	5.60 RPM
SRP007412_heart	0.03 RPM	5.82 RPM
SRP007412_kidney	0.12 RPM	4.62 RPM
SRP007412_liver	0.05 RPM	1.69 RPM
SRP007412_testis	0.05 RPM	2.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2346 was not detected

EST

No EST(s) were mapped for retro_mmus_2346 retrocopy.

TSS

No TSS is located nearby retro_mmus_2346 retrocopy 5' end.

Lab

retro_mmus_2346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2346 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013870	1 retrocopy	retro_dord_22,
Myotis lucifugus	ENSMLUG00000013000	2 retrocopies	retro_mluc_1384, retro_mluc_2298,
Mus musculus	ENSMUSG00000048222	2 retrocopies	retro_mmus_1147, retro_mmus_2346 ,
Mus musculus	ENSMUSG00000068479	2 retrocopies	retro_mmus_2386, retro_mmus_2638,
Otolemur garnettii	ENSOGAG00000010206	1 retrocopy	retro_ogar_1784,
Rattus norvegicus	ENSRNOG00000015984	1 retrocopy	retro_rnor_83,
Sarcophilus harrisii	ENSSHAG00000014628	1 retrocopy	retro_shar_107,
Ictidomys tridecemlineatus	ENSSTOG00000006967	2 retrocopies	retro_itri_1105, retro_itri_1494,
Tupaia belangeri	ENSTBEG00000005050	2 retrocopies	retro_tbel_3001, retro_tbel_3246,