RetrogeneDB ID: retro_mmus_3334

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:46713229..46713753(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aimp1
• Ensembl ID: ENSMUSG00000028029
• Aliases: Aimp1, 9830137A06Rik, AIMP1/p43, EMAPII, Emap2, Scye1, p43
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 [Source:MGI Symbol;Acc:MGI:102774]

Sequence

>retro_mmus_3334
CGGTCAGCAACAGCAAGTGCTGACTCTAAGCCTATCGGTGTATCGTGCCTGGAACTTCGAATTGCTTGTATCGTTACTGC
GGAGGAACACCCCAATGCAGATTCATTGTATGTCAAAGAAGTAGATGTGGGAAAAGCAGGCTCACGGACAGTCATCAGCA
GGCTGGTGAATCATGTTCCTCTAGAACAGATGCAAAATCAGATGGTGGTTTTTACTTTGTAATCTGAAGACTTCGAAAAT
GCAGGGAGTACTCTCTCAAGCAATGGTGATGGGTGCCAGTTCACTAGCGAAAGTGGAAATTCTGGCCCCTCCCAACGGAT
CCCTTCCTGGAGACAGAATCGCTTTTGATGCTTCCCCCTGGAGAGCCTGACAAGAAGCTGAACCCTAAGAAGATGATCTG
GGAGCAGATCCAGCCTGACCTGCACACCGGTGATGAGAATGGGGCCACATACAAAGGAGCTCCCTTTGAGGGGAAGGAGA
AGGGAGTTTGCAGGGCCCAAACCATGGCTAACGGCAGAATTAAA

Alignment

ORF - retro_mmus_3334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.84 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QSAAASTDSKPIDASRLDLRIGCIVTAKKHPDADSLYVEEVDVGEAAPRTVVSGLVNHVPLEQMQNRMVV
          .SA.AS.DSKPI..S.L.LRI.CIVTA..HP.ADSLYV.EVDVG.A..RTV.S.LVNHVPLEQMQN.MVV
Retrocopy RSATASADSKPIGVSCLELRIACIVTAEEHPNADSLYVKEVDVGKAGSRTVISRLVNHVPLEQMQNQMVV

Parental  -LLCNLKPAKMRGVLSQAMVMCASSPEKVEILAPPNGSVPGDRITFDAF-PGEPDKELNPKKKIWEQIQP
          .LLCNLK..KM.GVLSQAMVM.ASS..KVEILAPPNGS.PGDRI.FDA..PGEPDK.LNPKK.IWEQIQP
Retrocopy >LLCNLKTSKMQGVLSQAMVMGASSLAKVEILAPPNGSLPGDRIAFDAS>PGEPDKKLNPKKMIWEQIQP

Parental  DLHTNAECVATYKGAPFEVKGKGVCRAQTMANSGIK
          DLHT..E..ATYKGAPFE.K.KGVCRAQTMAN..IK
Retrocopy DLHTGDENGATYKGAPFEGKEKGVCRAQTMANGRIK

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	28.36 RPM
SRP007412_cerebellum	0.00 RPM	32.70 RPM
SRP007412_heart	0.00 RPM	33.84 RPM
SRP007412_kidney	0.00 RPM	31.51 RPM
SRP007412_liver	0.03 RPM	21.44 RPM
SRP007412_testis	0.00 RPM	51.50 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3334 was not detected

EST

No EST(s) were mapped for retro_mmus_3334 retrocopy.

TSS

No TSS is located nearby retro_mmus_3334 retrocopy 5' end.

Lab

retro_mmus_3334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3334 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334 ,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008,