RetrogeneDB ID: retro_mmus_1939

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:80132011..80132754(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083519
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Aida
• Ensembl ID: ENSMUSG00000042901
• Aliases: Aida, 2610208M17Rik, BC004835
• Description: axin interactor, dorsalization associated [Source:MGI Symbol;Acc:MGI:1919737]

Sequence

>retro_mmus_1939
AGGCAAAGCACCATAGGCAAAATTGCCACATGTTTAGAATTGCGAAGTGCAGCATTACAACCCACACAGTCCCAAGAAGA
GTTTAAACTGGAGGACCTGAAGAAGCTAGAACCAATCCTGAAGAATATTCTTACATATAATAAGGAATTCCCATTTGATG
TTCAACCTCTCCCATTAAGACGGATTTTAGCACCTGGTGAAGAAGAGAATTTGCAATTTGAAGAAGATGAAGAAAGAGAC
TCTGGAGCAGGACCTCCTGATGCTCTCTCTCTGCTAGAGTTTCCGGTACTTTATTGCCACGGTTGCCATCAGAACCAGGG
ATGACATTACTCACTATCAGGACTGAGAAAATTGGTCTGAAAGATGCCGGGCAGTGCATCGATCCGTACATCACAGTCAG
CGGGAAAGATTTGAATGGCATAGATTTAACTCCCGTACAAGATACTCCTGAGGCTTCAAGTAAAGAAGATTCTTGTGTTC
ATTTTAATGTGGACATTGAGGTCCAGAAACACGTTGAGAAGTTAACCAAAGGTGCTGCCTTCTTCTTTGAATTCAAACAT
TACAAGCTTAAAAAAAGGTTTACCAGGGCCAAGTGTTTTGCCTTTATGGAAATGGATGGAATTAAACCTGGGCCAATCGT
AATAGAACTATACAAGAAACCCACTGACTTTAAGAAAAAGAAATTGTAATTATTGACCAAGAAACTACTTTATCTTCATC
TACATCAAACTTTGAACAAGGAA

Alignment

ORF - retro_mmus_1939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.74 %
• Parental protein coverage: 80.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKKTIGKIATCLELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPIPLRRILAPGEEEN
          ...TIGKIATCLELRSAALQ.TQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQP.PLRRILAPGEEEN
Retrocopy RQSTIGKIATCLELRSAALQPTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPLPLRRILAPGEEEN

Parental  LEFEE-DEEGGAGAGPPD-SFSARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLN
          L.FEE..E.......P...S.SARV.GTLLPRLPSEPGMTLLTIR.EKIGLKDAGQCIDPYITVS.KDLN
Retrocopy LQFEEDEERDSGAGPPDA<SLSARVSGTLLPRLPSEPGMTLLTIRTEKIGLKDAGQCIDPYITVSGKDLN

Parental  GIDLTPVQDTPVASRKEDTYVHFNVDIELQKHVERLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIK
          GIDLTPVQDTP.AS.KED..VHFNVDIE.QKHVE.LTKGAA.FFEFKHYK.KKRFT..KCFAFMEMD.IK
Retrocopy GIDLTPVQDTPEASSKEDSCVHFNVDIEVQKHVEKLTKGAAFFFEFKHYKLKKRFTRAKCFAFMEMDGIK

Parental  PGPIVIELYKKPTDFKRKKLQLLTKKPLYLHLHQSLHKE
          PGPIVIELYKKPTDFK.KKL.LLTKK.LYLHLHQ.L.KE
Retrocopy PGPIVIELYKKPTDFKKKKL*LLTKKLLYLHLHQTLNKE

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	28.71 RPM
SRP007412_cerebellum	0.00 RPM	21.58 RPM
SRP007412_heart	0.00 RPM	15.47 RPM
SRP007412_kidney	0.00 RPM	17.17 RPM
SRP007412_liver	0.00 RPM	6.12 RPM
SRP007412_testis	0.00 RPM	13.45 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1939 was not detected

EST

No EST(s) were mapped for retro_mmus_1939 retrocopy.

TSS

No TSS is located nearby retro_mmus_1939 retrocopy 5' end.

Lab

retro_mmus_1939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448,
Mus musculus	ENSMUSG00000042901	3 retrocopies	retro_mmus_1939 , retro_mmus_3098, retro_mmus_763,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688,
Pteropus vampyrus	ENSPVAG00000010662	1 retrocopy	retro_pvam_940,