RetrogeneDB ID: retro_mmus_3229

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:97427714..97429110(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081111
• 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_3229
ATGGTTATGGAGAAGCCTAGTCCCCTGCTGGTCAGGCGGGAGTTTGTGCGACAGTACTACACCCTGCTGAACCAGGCCCT
GGACATGCTGCACAGATTTTATGGAAAGAACTCTTCCTATGCCCACGGGGGCTTGGATTCCAACGGGAAGCCAGCAGATG
CAGTCTACGGGAAGAAGGAAATCCACAGGAAAGTGATGTCACAAAACTTCACCAACTGCCACACCAAGATCTGCCACGTG
GATGCTCACGCAACTCTGAATGACGGGGTGGTTGTCCAAGTGATGGGGCTACTGTCCAACAACAACCAGGCTCTGCGGAG
GTTCATGCAGACCTTTGTCCTTGCTCCTGAGGGCTCTGCTGCCAACAAATTCTATGTTCACAACGACATCTTCAGATACC
AAGATGAGGTCTTCGGTGGCTTTGTCACAGAGCCTCAAAAGGAATCCGAGGAAGAAGTAGAAGAACCTGAAGAAAGACAG
CAGACACCAGAGGTGGTGCCTGATGATTCTGGAACTTTCTATGATCAGACTGTCAGCAATGACTTGGAGGAGCATTTAGA
GGAGCCTGTAGTGGAACCAGAACCGGAGCCAGAGCCGGAGCCAGAGCCGGAACCTGTGTCCAACATTCAAGAGGACAAGC
CTGAGGCTGCATTGGAAGAAGCTGCTCCCGACGATGTGCAGAAGAGCACTTCCCCGACCCCGGCTGACGTGGCCCCGGCA
CAGGAGGACTTGAGGACGTTTTCTTGGACATCTATGACGAGTAAGAACCTTCCTCCCAGTGGGGCTGTTCCAGTGACGGG
GACATCACCTCATGTGGTCAAAGTGCCAGCGTCACAGCCCGGTCCAGAATCTAAACCTGACTCTCAGATCCCACCACAAA
GGCCTCAGAGAGATCAGAGAGTTCGAGAGCAGCGAATCAATATCCCTCCTCAGAGAGGACCCCGACCAATCCGTGAGGCT
GGTGAACCAGGAGATGTGGAACCTCGAAGGATGGTGAGGCACCCTGACAGTCACCAGCTCTTCACTGGAAACCTGCCACA
TGAAGTTGACAAGTCGGAACTGAAGGATTTTTTTCCAAAATTTTGGCAATGTGGTGGAGCTGCGCATCAACAGTGGTGGG
AAGTTACCCAATTTCGGTTTTGTTGTGTTTGATGATTCTGAACCTGTTCAGAAGGTCCTTAATAATAGGCCCATCATGTT
CCGAGGCGCGGTCCGCCTGAATGTGGAAGAGAAGAAGACTCGAGCTGCCAGAGAAGGCGACCGCAGGGATAACCGCCTTC
AGGGACCTGGAGGCCCCCGTGGTGGGCCGAGTGGTGGGATGAGAGGTCCTTCCCGTGGAGGCATGGTGCAGAAACCAGGC
TTTGGCGTGGGCAGGGGAATTACAACTCCAAGGCAG

Alignment

ORF - retro_mmus_3229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYAHGGLDSNGKPADAVYGQKEIHRKVMSQNF
          MVMEKPSPLLV.REFVRQYYTLLNQA.DMLHRFYGKNSSYAHGGLDSNGKPADAVYG.KEIHRKVMSQNF
Retrocopy MVMEKPSPLLVRREFVRQYYTLLNQALDMLHRFYGKNSSYAHGGLDSNGKPADAVYGKKEIHRKVMSQNF

Parental  TNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFGG
          TNCHTKI.HVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGS.ANKFYVHNDIFRYQDEVFGG
Retrocopy TNCHTKICHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSAANKFYVHNDIFRYQDEVFGG

Parental  FVTEPQEESEEEVEEPEERQQTPEVVPDDSGTFYDQTVSNDLEEHLEEPVVEPEPEPEPEPEPEPVSDIQ
          FVTEPQ.ESEEEVEEPEERQQTPEVVPDDSGTFYDQTVSNDLEEHL....................S.IQ
Retrocopy FVTEPQKESEEEVEEPEERQQTPEVVPDDSGTFYDQTVSNDLEEHLXXXXXXXXXXXXXXXXXXXXSNIQ

Parental  EDKPEAALEEAAPDDVQKSTSPAPADVAPAQEDLRTFSWASVTSKNLPPSGAVPVTGTPPHVVKVPASQP
          EDKPEAALEEAAPDDVQKSTSP.PADVAPAQEDLRTFSW.S.TSKNLPPSGAVPVTGT.PHVVKVPASQP
Retrocopy EDKPEAALEEAAPDDVQKSTSPTPADVAPAQEDLRTFSWTSMTSKNLPPSGAVPVTGTSPHVVKVPASQP

Parental  RPESKPDSQIPPQRPQRDQRVREQRINIPPQRGPRPIREAGEPGDVEPRRMVRHPDSHQLFIGNLPHEVD
          .PESKPDSQIPPQRPQRDQRVREQRINIPPQRGPRPIREAGEPGDVEPRRMVRHPDSHQLF.GNLPHEVD
Retrocopy GPESKPDSQIPPQRPQRDQRVREQRINIPPQRGPRPIREAGEPGDVEPRRMVRHPDSHQLFTGNLPHEVD

Parental  KSELKD-FFQNFGNVVELRINSGGKLPNFGFVVFDDSEPVQKVLSNRPIMFRGAVRLNVEEKKTRAAREG
          KSELKD.FFQNFGNVVELRINSGGKLPNFGFVVFDDSEPVQKVL.NRPIMFRGAVRLNVEEKKTRAAREG
Retrocopy KSELKD>FFQNFGNVVELRINSGGKLPNFGFVVFDDSEPVQKVLNNRPIMFRGAVRLNVEEKKTRAAREG

Parental  DRRDNRLRGPGGPRGGPSGGMRGPPRGGMVQKPGFGVGRGITTPRQ
          DRRDNRL.GPGGPRGGPSGGMRGP.RGGMVQKPGFGVGRGITTPRQ
Retrocopy DRRDNRLQGPGGPRGGPSGGMRGPSRGGMVQKPGFGVGRGITTPRQ

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	0.09 RPM	51.45 RPM
SRP007412_heart	0.47 RPM	92.49 RPM
SRP007412_kidney	0.21 RPM	84.14 RPM
SRP007412_liver	0.08 RPM	51.42 RPM
SRP007412_testis	4.62 RPM	40.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3229 was not detected

EST

No EST(s) were mapped for retro_mmus_3229 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_145737	122 libraries	298 libraries	626 libraries	22 libraries	4 libraries

The graphical summary, for retro_mmus_3229 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3229 has 0 orthologous retrocopies within eutheria group .

---

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,