RetrogeneDB ID: retro_mmus_3688

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:113226570..113227320(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081831
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: G3bp1
• Ensembl ID: ENSMUSG00000018583
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 1 [Source:MGI Symbol;Acc:MGI:1351465]

Sequence

>retro_mmus_3688
ATCGCTATGGAGAAGCCTAGTCCCCTGCTGGTCTGAGGGGAGTCTGTGTGGCAGTGCTACACCCTGCTGAACCAGGCCCC
AGACACACTGCACAGATTTTATGGAATGAACTCTTCCTATGCACACAAGGGCTTGGATTCCAATGGGAAGCCAGCAGCAG
TCTACAGGCAGAAAGAAATCCACAGGAAAGTGATGTCACAAAACTTCACCAACTGCTACACCAAGATCTGCCTTGTGGAT
GCTCACACAACTCTGAATGGCAGGGTGGTGTTCCAAGTGATGGGGCTATGGTCCAACAACAACCAGGCTCTGCGGAGGTT
CATGAAGAACTTTGTCCTTGCACCTGAGGGCTCTGTTGCCAACACATTCTATGTTCACAACGACATCTTCAGATACCAAG
ATGAGGCCTTTGGTGGCTTTGTCACAGATCCTCAAGAGGAATCCGAGGAAGTAGTAGAGGAACCTGAAGAAAGAGAGCAG
ACACCAGAGGTGATGTCTGATGACTCTGGAACTCTCTATGGTCAGACTGTCAGCAATGACTTGGAGGAGCATTTAGAGGA
GCCTGTTGTAGTATCAGAACCAGAGCCTGAGCCAGAGTCAGAGCTGGAACCTGTGCCTGACACCTGAGAGGACAAAACTG
AGCCAGCATTGGAGGAACCTGCTCCTGAGGACATGCAGAAGAGGGCTACCCTTGCCCTGACAGACGTGGCCCCAGCACAG
GAGGACTTAGGGTTATTTTCTTGGGCATCT

Alignment

ORF - retro_mmus_3688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.68 %
• Parental protein coverage: 53.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYAHGGLDSNGKPADAVYGQKEIHRKVMSQNF
          ..MEKPSPLLV..E.V.Q.YTLLNQAPD.LHRFYG.NSSYAH.GLDSNGKPA.AVY.QKEIHRKVMSQNF
Retrocopy IAMEKPSPLLV*GESVWQCYTLLNQAPDTLHRFYGMNSSYAHKGLDSNGKPA-AVYRQKEIHRKVMSQNF

Parental  TNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFGG
          TNC.TKI..VDAH.TLN..VV.QVMGL.SNNNQALRRFM..FVLAPEGSVAN.FYVHNDIFRYQDE.FGG
Retrocopy TNCYTKICLVDAHTTLNGRVVFQVMGLWSNNNQALRRFMKNFVLAPEGSVANTFYVHNDIFRYQDEAFGG

Parental  FVTEPQEESEEEVEEPEERQQTPEVVPDDSGTFYDQTVSNDLEEHLEEPVVEPEPEPEPEPEPEPVSDIQ
          FVT.PQEESEE.VEEPEER.QTPEV..DDSGT.Y.QTVSNDLEEHLEEPVV..EPEPEPE.E.EPV.D..
Retrocopy FVTDPQEESEEVVEEPEEREQTPEVMSDDSGTLYGQTVSNDLEEHLEEPVVVSEPEPEPESELEPVPDT*

Parental  EDKPEAALEEAAPDDVQKSTSPAPADVAPAQEDLRTFSWAS
          EDK.E.ALEE.AP.D.QK....A..DVAPAQEDL..FSWAS
Retrocopy EDKTEPALEEPAPEDMQKRATLALTDVAPAQEDLGLFSWAS

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	58.22 RPM
SRP007412_cerebellum	0.00 RPM	51.45 RPM
SRP007412_heart	0.00 RPM	92.49 RPM
SRP007412_kidney	0.00 RPM	84.14 RPM
SRP007412_liver	0.00 RPM	51.42 RPM
SRP007412_testis	0.00 RPM	40.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3688 was not detected

EST

No EST(s) were mapped for retro_mmus_3688 retrocopy.

TSS

No TSS is located nearby retro_mmus_3688 retrocopy 5' end.

Lab

retro_mmus_3688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3688 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Mus musculus	ENSMUSG00000018583	3 retrocopies	retro_mmus_1389, retro_mmus_3229, retro_mmus_3688 ,
Nomascus leucogenys	ENSNLEG00000016470	1 retrocopy	retro_nleu_1814,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,