RetrogeneDB ID: retro_mmus_1389

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:37171038..37171795(-)
• Located in intron of: None

Retrocopy information

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

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_1389
AAGCCTGAGCCTGCATTGGAAGAATCTGCTCCCGAGAATGTACAGAAGAGTAAACTCCGACCCCGGCAGATGTGGCCCCG
GCACAGGAGGACTTGAGGACATTTTCTTGGGCATCTGTGACTAGTAAGAACCTTCCTCCCAGGGGGGCTGTTCCAGTGAC
GGAGACACCACCTCATGTGGTCAAAGTGCCAGCGTCACAGCCCTGTCCAGAATCTAAACCTGACTCTCAGATTCCACCAC
AAAGGCCTCAGAGAGATCAGCGAGTTTGAGAGCAGCGAAATCAATATTCCTCCTCAGAGAGGATCCCGACCAATCCGTGA
GGCTGGTAAACCAGGAGATGTGGAACCTCGAAGGATGGTGAGGCACCCTGACAGTCACCAGCTCTTCATTGGGAACCTGC
CACATGAGACGGTTGACAAGTCGGAACTGAAGAATTTTTTTCCAAAATGTTGGCAATGTGGTGGAACTGCGCATCAACAG
TGGTGGAAAGTTACCCAATTTCGGTTTTGTTGTGTTTGATGATTCTGAACCTGTTCAGAAGGTCCTTAATAGGACCTTCA
TGTTCCAAGGCGCAGTCCGCCTGAATGTGGAAGAGAAGACTCGAACTGCCAGAGAAGGCGACCGCAGGGATAACCGCCTT
TGGGGACCTGGAGGCCCCGGTGATGGATCGAGTGGTGGGATAAGAGGCTCTCCCCGTGGAGGCATGGTGCAGAAACCAGG
CTTTGGTGTGGGCAGGGGGATTACAACTCCAAGGCAG

Alignment

ORF - retro_mmus_1389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 54.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KPEAALEEAAPDDVQKST-SPAPADVAPAQEDLRTFSWASVTSKNLPPSGAVPVTGTPPHVVKVPASQPR
          KPE.ALEE.AP..VQKS...P.PADVAPAQEDLRTFSWASVTSKNLPP.GAVPVT.TPPHVVKVPASQP.
Retrocopy KPEPALEESAPENVQKSK<TPTPADVAPAQEDLRTFSWASVTSKNLPPRGAVPVTETPPHVVKVPASQPC

Parental  PESKPDSQIPPQRPQRDQRVREQR-INIPPQRGPRPIREAGEPGDVEPRRMVRHPDSHQLFIGNLPHE-V
          PESKPDSQIPPQRPQRDQRV.EQR.INIPPQRG.RPIREAG.PGDVEPRRMVRHPDSHQLFIGNLPHE.V
Retrocopy PESKPDSQIPPQRPQRDQRV*EQR>INIPPQRGSRPIREAGKPGDVEPRRMVRHPDSHQLFIGNLPHETV

Parental  DKSELKD-FFQNFGNVVELRINSGGKLPNFGFVVFDDSEPVQKVLSNRPIMFRGAVRLNVEEKKTRAARE
          DKSELK..FFQN.GNVVELRINSGGKLPNFGFVVFDDSEPVQKVL.NR..MF.GAVRLNVEE.KTR.ARE
Retrocopy DKSELKN>FFQNVGNVVELRINSGGKLPNFGFVVFDDSEPVQKVL-NRTFMFQGAVRLNVEE-KTRTARE

Parental  GDRRDNRLRGPGGPRGGPSGGMRGPPRGGMVQKPGFGVGRGITTPRQ
          GDRRDNRL.GPGGP..G.SGG.RG.PRGGMVQKPGFGVGRGITTPRQ
Retrocopy GDRRDNRLWGPGGPGDGSSGGIRGSPRGGMVQKPGFGVGRGITTPRQ

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	58.22 RPM
SRP007412_cerebellum	0.00 RPM	51.45 RPM
SRP007412_heart	0.00 RPM	92.49 RPM
SRP007412_kidney	0.02 RPM	84.14 RPM
SRP007412_liver	0.00 RPM	51.42 RPM
SRP007412_testis	0.69 RPM	40.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1389 was not detected

EST

No EST(s) were mapped for retro_mmus_1389 retrocopy.

TSS

No TSS is located nearby retro_mmus_1389 retrocopy 5' end.

Lab

retro_mmus_1389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1389 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,