RetrogeneDB ID: retro_mmus_2638

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:28000564..28001306(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mfap1a
• Ensembl ID: ENSMUSG00000068479
• Aliases: Mfap1a, 4432409M24Rik, Mfap1
• Description: microfibrillar-associated protein 1A [Source:MGI Symbol;Acc:MGI:1914782]

Sequence

>retro_mmus_2638
ATGTGGGTCCCAAGCACACTCATGAAGCAGCCGCCCACCCAGTCTAGGGCTGGGGCCATCCAGGTTCGCAATGAGAGAGG
CGAGATTTCAATGGAAAAGGTGAAGGTAAAACGTTATGTGTCCGGAAAGAGACCAGATTATGCCCCTATGGAGTCCTCAG
ATGAAGAGGATGGAGAATTTCAGTTCATTAAGAAAGCTAAGGAACAAGGAACAGGGCCTGAGGAATAAATAGGAGGAGGA
CTCATCCAGTGACCCCCCGACTTCGGCGGTTACAGAACCACATTAGTGAAGGTGTGGAAGAGAGATTGGCTCGACACAGA
AAAATAGTGGAACCTGAAGTAGTAGGAGAACGCGACTCAGAAGTACAAGGAGATGCTTGGCGCATGGGATGAGAAGATAG
CAGTGAGGAAGAGGAGGAAGAGATTGATAATGAAGAAATAGAACGGCGCCGTGGCATGATGCGTCAGCGAGCACAGGAGA
GGAAAAATGAAGAGATGGAAGTCATGGAGGTGGAAGATGAAGCGCGCTCTGGGGAGGAGTCTGAGTCAGAGTCTGACTCT
GAGGAGTACCCAGACATGAGGATGAAATGGAGCCTCGACTTAAGCCTGTCTTCATTCGAAAGAAGGATCGGGTGACAGTT
CAAGAACGAGAAGCTGAAGCATTGAAACAGAAGGAACTGGAACAAGAAGCAAAACGCATGGCTGAGGAGCGGCGCAAGTA
CACCCTCAAGATTGTAGAAGAG

Alignment

ORF - retro_mmus_2638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.8 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSVPSALMKQPPIQSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFI-KKAKEQ
          M.VPS.LMKQPP.QS.AGA..VRNE.GEISMEKVKVKRYVSGKRPDYAPMESSDEED.EFQFI..K....
Retrocopy MWVPSTLMKQPPTQSRAGAIQVRNERGEISMEKVKVKRYVSGKRPDYAPMESSDEEDGEFQFI>RKLRNK

Parental  EAEPEEQ-EEDSSSDP-RLRRLQNRISEDVEERLARHRKIVEPEVVGESDSEVEGDAWRLEREDSSEEEE
          E.......EEDSSSDP.RLRRLQN.ISE.VEERLARHRKIVEPEVVGE.DSEV.GDAWR...EDSSEEEE
Retrocopy EQGLRNK*EEDSSSDP>RLRRLQNHISEGVEERLARHRKIVEPEVVGERDSEVQGDAWRMG*EDSSEEEE

Parental  EEIDDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEESESESEYEEYTD-SEDEMEPRLKPVFIRK
          EEID.EEIERRRGMMRQRAQERKNEEMEVMEVEDE.RSGE.........EY.D..EDEMEPRLKPVFIRK
Retrocopy EEIDNEEIERRRGMMRQRAQERKNEEMEVMEVEDEARSGEXXXXXXXXXEYPD<HEDEMEPRLKPVFIRK

Parental  KDRVTVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEE
          KDRVTVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEE
Retrocopy KDRVTVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEE

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	14.27 RPM
SRP007412_cerebellum	0.04 RPM	17.80 RPM
SRP007412_heart	0.12 RPM	15.10 RPM
SRP007412_kidney	0.12 RPM	14.90 RPM
SRP007412_liver	0.00 RPM	6.23 RPM
SRP007412_testis	0.09 RPM	8.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2638 was not detected

EST

No EST(s) were mapped for retro_mmus_2638 retrocopy.

TSS

No TSS is located nearby retro_mmus_2638 retrocopy 5' end.

Lab

retro_mmus_2638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2638 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,