RetrogeneDB ID: retro_mmus_1147

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:115163606..115164482(-)
• Located in intron of: None

Retrocopy information

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

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_1147
GAGAGATTAGAGCGGCACCGTGACATGACGTGTCAGCGAGCACAGGAGAGAAAAAAATGAAGAGATGAAAGTCATGGAGA
TGGAAGATGAGGGACGCTCTGGGGAGGAGTCTGAGTCGTTAGAGTCTGAGGAGTACACAGACAGCGAAGGTGAAATGGAG
CCTCGACTTAAGCCTGTCTTCATTTGAAAGAAGGATCAGGTGACAGTTCAAGAATGAGAACCTGAAGCCCTAAAACATAA
GGAGCTTGAACAGGAAGCAAAGCGTATGGCTGAGGAGCTGCGCAAGTACACACCCAAAATTGTAGAAGAAACCAAGAAGG
AGCTAGAGGAGAACAAGCGGTCCCTTGCCGCCCTGGATGCACTCAGTACCGATGATGAAAATGAGGAGGAGGAGTACTAG
GCGTGAAAACTCCGAGAGCTCAAAAGAATCAAGTGCGACAGAGAAGACCTAGAAGTGCTTGAAACGGAGAAAGCAGACAT
TGAATGCATGAGAAACCTGACTGAGGAAGAAAGGCAGGCGGAACTTCGGACAATGTCATTACCAACAAAGCTATTAAAGG
CAAATAAAAGTTTTTACAAAAGTATTCTCACCGAGGTACCTTCTTCATGAACGAAGATGAAGAAGTCTACAAGAGAGATT
TTAGTGCGCCTACTCTTGAGGACCATTTCAACAAAACCATTCTTCCAAAAGCCATGCAGGTCAAGAATTTCGGAAGGTCT
GGTCGCACCAAGCACACCCACCTTGTAGATCAAGATACCACTTCCTTTGACTCTGCATGGGGCCAAGAGAGTGCACAGAA
CACAAAATTTGTGAAACAAAAGGCAGCAGGGGTCCCAGATGTAGTTGAATGACCCTCTACCAAGAAGAAAACCACC

Alignment

ORF - retro_mmus_1147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 67.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEIERRRGMMRQRAQERK-NEEMEVMEVEDEGRSGEESESESEYEEYTDSEDEMEPRLKPVFIRKKDRVT
          E..ER.R.M..QRAQERK.NEEM.VME.EDEGRSGEESES..E.EEYTDSE.EMEPRLKPVFI.KKD.VT
Retrocopy ERLERHRDMTCQRAQERK>NEEMKVMEMEDEGRSGEESES-LESEEYTDSEGEMEPRLKPVFI*KKDQVT

Parental  VQEREAEALKQKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEAWKV
          VQE.E.EALK.KELEQEAKRMAEE.RKYT.KIV.EETKKELEENKRSLAALDAL.TDDEN.EEEY.A.K.
Retrocopy VQE*EPEALKHKELEQEAKRMAEELRKYTPKIV-EETKKELEENKRSLAALDALSTDDENEEEEY*A*KL

Parental  RELKRIKREREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKF-LQKYYHRGAFFMD
          RELKRIK..RED.E.LE.EKA.IE.MRNLTEEER.AELR........K..K....F.LQKY.HRG.FFM.
Retrocopy RELKRIKCDREDLEVLETEKADIECMRNLTEEERQAELRTMS--LPTKLLKANKSF<LQKYSHRGTFFMN

Parental  EDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFFKQK
          EDEEVYKRDFSAPTLEDHFNKTILPK.MQVKNFGRSGRTK.THLVDQDTTSFDSAWGQESAQNTKF.KQK
Retrocopy EDEEVYKRDFSAPTLEDHFNKTILPKAMQVKNFGRSGRTKHTHLVDQDTTSFDSAWGQESAQNTKFVKQK

Parental  AAGVRDVFERPSAKKRKT
          AAGV.DV.E.PS.KK..T
Retrocopy AAGVPDVVE*PSTKKKTT

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	9.39 RPM
SRP007412_cerebellum	0.00 RPM	5.60 RPM
SRP007412_heart	0.00 RPM	5.82 RPM
SRP007412_kidney	0.00 RPM	4.62 RPM
SRP007412_liver	0.00 RPM	1.69 RPM
SRP007412_testis	0.00 RPM	2.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1147 was not detected

EST

No EST(s) were mapped for retro_mmus_1147 retrocopy.

TSS

No TSS is located nearby retro_mmus_1147 retrocopy 5' end.

Lab

retro_mmus_1147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1147 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,