RetrogeneDB ID: retro_mmus_3551

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:154774452..154775435(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082197
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nipa2
• Ensembl ID: ENSMUSG00000030452
• Aliases: Nipa2, 2600017P10Rik, 3830408P04Rik, AB041581
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 homolog (human) [Source:MGI Symbol;Acc:MGI:1913918]

Sequence

>retro_mmus_3551
AAAAAAGGCCTTCTGCGAATTGCCAGGAAAGGCTCCATGAGTGCAGGTCAAGGAGGCCATGCATATTTTAATGAATGGTT
GTGGTGGGCTGGACTGCTGTCAATGGGAGCCGGTGATGTAACTAATTTTGCTGCATATGCATTTGCTCCGGCCACATTAG
TGACTCCACTAGTTACGCTCAGCGTCCTTGTAAGTGCCATTCTGTCTTCATACTTCCTAAATGAAAGACTTAATCTTCAT
GGGAAAATTGGGTGTTTGCTAAGTATTCTAGGGTCTACAGTTATGATCATTCATGCTCCAAAGAAAGAGGAGATTGAGAC
CTTAAATGAAATGTCACATAAGTTAGGTGATCCAGGTTTTGTGGTCTTTGCAACATTTGTGGTCATTGTGGCCTTGATAT
TCATCTTTGTGGTGGGACCTCGACATGGACAGACAAGCATTCTTGTGTATATAACAATCTACTCTGTGATTGGAGCATTT
TCAGTCTCCTGTGTGAAGAGTTTGGGTATTGCCATAAAAGAGTTGTTGGCTGGAAAGCCTGTTCTGCAGCACCCCTCACC
TGGATTCTACTGTTTAGCCTTGCAGTCTGTGTGAGCAAAAAGATTAATTACCTAAACCAGGCTCTGGACATTTTCAACAC
TTCCATTGTGACTCCAATATATTATGTGTTCTTTACAACTTCAGTTTTGACTTGTTCAGCTATTCTTTTTAAAGAATGGC
CGGATATGCCTGTTGATGATGTCATTGGGACTTTGAGTGGCTTCTTCACAATCATTGTGGGGATATTTTTGTTGCATGCC
TTTAAAGATGTCAGTGTTAGTCTAGCAAGTCTGCCAGTATATTTTCTAAAAGATGAAAAGGCAATGAATGGCAATCTTAT
TAGTATGTATGAAGTTCTTAATAATAATGAAGAAGACTTAACCTGTGGAATTGAAAACACTGGTGAAAATATTTCCCGTA
GGAATGGAAATCTGACATCTTTT

Alignment

ORF - retro_mmus_3551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.49 %
• Parental protein coverage: 91.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKGLLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGAGEVANFAAYAFAPATLVTPLGALSVLVSAILSS
          KKGLLR.ARKGSM.AGQGGHAY..EWLWWAGLLSMGAG.V.NFAAYAFAPATLVTPL..LSVLVSAILSS
Retrocopy KKGLLRIARKGSMSAGQGGHAYFNEWLWWAGLLSMGAGDVTNFAAYAFAPATLVTPLVTLSVLVSAILSS

Parental  YFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEEIETLNEMSHKLGDPGFVVFATFVVIVALIFIFVVGP
          YFLNERLNLHGKIGCLLSILGSTVM.IHAPK.EEIETLNEMSHKLGDPGFVVFATFVVIVALIFIFVVGP
Retrocopy YFLNERLNLHGKIGCLLSILGSTVMIIHAPKKEEIETLNEMSHKLGDPGFVVFATFVVIVALIFIFVVGP

Parental  RHGQTNILVYITICSVIGAFSVSCVKGLGIAIKELLAGKPVLQH-PLAWILLFSLVVCVSTQINYLNRAL
          RHGQT.ILVYITI.SVIGAFSVSCVK.LGIAIKELLAGKPVLQH.PL.WILLFSL.VCVS..INYLN.AL
Retrocopy RHGQTSILVYITIYSVIGAFSVSCVKSLGIAIKELLAGKPVLQH<PLTWILLFSLAVCVSKKINYLNQAL

Parental  DIFNTSIVTPIYYVFFTTSVLTCSAILFKEWQDMPVDDVIGTLSGFFTIIVGIFLLHAFKDVSFSLASLP
          DIFNTSIVTPIYYVFFTTSVLTCSAILFKEW.DMPVDDVIGTLSGFFTIIVGIFLLHAFKDVS.SLASLP
Retrocopy DIFNTSIVTPIYYVFFTTSVLTCSAILFKEWPDMPVDDVIGTLSGFFTIIVGIFLLHAFKDVSVSLASLP

Parental  VSFRKDEKAMNGNLSSMYEVLNNNEDDLPCGIEHTGENISRRNGNLPSF
          V.F.KDEKAMNGNL.SMYEVLNNNE.DL.CGIE.TGENISRRNGNL.SF
Retrocopy VYFLKDEKAMNGNLISMYEVLNNNEEDLTCGIENTGENISRRNGNLTSF

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	24.34 RPM
SRP007412_cerebellum	0.00 RPM	15.20 RPM
SRP007412_heart	0.00 RPM	16.78 RPM
SRP007412_kidney	0.02 RPM	23.73 RPM
SRP007412_liver	0.00 RPM	22.23 RPM
SRP007412_testis	0.00 RPM	9.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3551 was not detected

EST

No EST(s) were mapped for retro_mmus_3551 retrocopy.

TSS

No TSS is located nearby retro_mmus_3551 retrocopy 5' end.

Lab

retro_mmus_3551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3551 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551 ,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,