RetrogeneDB ID: retro_mmus_2386

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:111290186..111291113(+)
• Located in intron of: ENSMUSG00000061298

Retrocopy information

• Ensembl ID: ENSMUSG00000081068
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2386
GAGAAAGGTGAGATCTCAATGGAAACGGTGAAGGTGAAACGTTATGTGTCTGGAAAGAGACCAGATTATGCCCCTATGGA
GTCCTCAGATGAAGAGGATGAAGAATTTCAGTTCATTAAGAAAGCTAAGGAACAAGAAGCAGAGCCTGAGGAACAGGAGG
AGGATTCATCCAGTGACCCCCGTCTTCGGCGGTTACAGAACCGCATCAGTGAAGATGTGGAAGAGAGAAAGGATCAGATT
ACAGTTCAAGGATGAGAAGCTGAAGCATTGAAACAGAAGGAACTGGAACAAGAAGCAAAATGCGTGGCTGAGGAGTGGCA
CAAGTACACCCTCAAGGTTGTAGAAGAAGAGACCAAGAAAGAGCTAGAGGAGAACAAGCGGTCCCTTGCCGCCCTGGATG
CACTCAATACTGATGATGAAAATGATGAGGAGGAGTACGAGGCGTGGAAAGTCCGCTGGCTCAAAAGAATCAAGTGGGAG
AGAGAAGACTGAGAAGCGCTTGAAAAGGAGAAAGCAGAAATTGAACGCATGAGAAACCTGACTGAGGAAGAAAGGCGGGC
TGAACTTCAGGCAAATGGCAAAGTCATTACCAACAAAGCTGTTAAAGGCAAATACAAGTTTCCACAGAAGTATTATCACC
GAGGTGCCTTCTTCATGGATGAGAATGAAGAAGTCTACAAGAGAGATTTTAGTGCACCTACTCTTGAGGACCATTTCAAC
AAAACCATTCTTCCTAGAGTCATGCAGGTCAAGAATTTTGGACGGTCTGGTCGCACCAAGTACACCCACCTTGTGGATCA
AGATACCACTTCCTTTGACTCTGCATGGGGCCAAGAGAGTGCCCAGAACACAAAATTCTTTAAACAAAAGGCAGCAGGGG
TATGAGATGTATTTGAGTGACCATCTGCCAAGAAGAGGAAAACCACT

Alignment

ORF - retro_mmus_2386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.76 %
• Parental protein coverage: 69.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEEIDDEEIERRRGMMRQRAQERKNEEMEVMEVEDEG-RSGEESESESEYEEYTDSED----EMEPRLK
          E..EI..E.....R.....R......E.......E........E.E.E.E..E...S.D........R..
Retrocopy EKGEISMETVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAKEQEAEPEEQEEDSSSDPRLRRLQNRIS

Parental  PVFIRKKDRVTVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDE
          ......KD..TVQ..EAEALKQKELEQEAK..AEE..KYTLK.VEEETKKELEENKRSLAALDALNTDDE
Retrocopy EDVEERKDQITVQG*EAEALKQKELEQEAKCVAEEWHKYTLKVVEEETKKELEENKRSLAALDALNTDDE

Parental  NDEEEYEAWKVRELKRIKREREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQK
          NDEEEYEAWKVR.LKRIK.ERED.EALEKEKAEIERMRNLTEEERRAEL.ANGKVITNKAVKGKYKF.QK
Retrocopy NDEEEYEAWKVRWLKRIKWERED*EALEKEKAEIERMRNLTEEERRAELQANGKVITNKAVKGKYKFPQK

Parental  YYHRGAFFMDEDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQES
          YYHRGAFFMDE.EEVYKRDFSAPTLEDHFNKTILP.VMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQES
Retrocopy YYHRGAFFMDENEEVYKRDFSAPTLEDHFNKTILPRVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQES

Parental  AQNTKFFKQKAAGVRDVFERPSAKKRKTT
          AQNTKFFKQKAAGV.DVFE.PSAKKRKTT
Retrocopy AQNTKFFKQKAAGV*DVFE*PSAKKRKTT

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	14.27 RPM
SRP007412_cerebellum	0.09 RPM	17.80 RPM
SRP007412_heart	0.09 RPM	15.10 RPM
SRP007412_kidney	0.19 RPM	14.90 RPM
SRP007412_liver	0.00 RPM	6.23 RPM
SRP007412_testis	0.14 RPM	8.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2386 was not detected

EST

No EST(s) were mapped for retro_mmus_2386 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_99177	597 libraries	415 libraries	56 libraries	0 libraries	4 libraries

The graphical summary, for retro_mmus_2386 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2386 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,