RetrogeneDB ID: retro_mmus_1547

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:15597927..15598445(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Itgb3bp
• Ensembl ID: ENSMUSG00000028549
• Aliases: Itgb3bp, 4930471O16Rik, AU022583
• Description: integrin beta 3 binding protein (beta3-endonexin) [Source:MGI Symbol;Acc:MGI:1914983]

Sequence

>retro_mmus_1547
ATGCCAGTTAAAAGATCACTGAAACTGAATGATCAGTTTGAAAAAGAACTCATTTAGTCCTTCAAAAATCGTGAGGAAGA
AAAGTATTACAGCGTATTCTCCTACTACTGGAACTTATCAATTGAGCCCATTTTCTTCTCCCGCAATCCCCAAAGAACAG
GAGCACAGAAACGAACCATCAAATGAAACAAGGAACTTGAGCTCCTGTAAGACAGGAGTCCACAGTGAAAGACAGTGATG
GATTCATGGTGTTGCTATCTAAAATTGAGATATCATCAGAGAAAACCATGGAGATAATGAAAAATCTAAGTAGTATACAG
ACTTTGGAAGGCAACAGACAACTTGAAGATCTCATTGGTGTTTCCCTAGTACCATGCTCCTTAAAAAGAGAAGCAAGGAA
AGCCAAAGAACTAATGACTAAAGTAATAAAACAAAAGTTGTTTGAAAAGAAAAAATGAAGAATTACTCCCAAAGATCATC
ATGTTGACAGCTTTGAATTCCTTAAAGCCATTTTGAAC

Alignment

ORF - retro_mmus_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPVKRSLKLDDQFEK-NSFSPSKIVRKKSITAYSPTTGTYQLSP-FSSPATPKEQEHRNGPSNETRKRSN
          MPVKRSLKL.DQFEK.NSFSPSKIVRKKSITAYSPTTGTYQLSP.F..P..PK....R....N...K...
Retrocopy MPVKRSLKLNDQFEK>NSFSPSKIVRKKSITAYSPTTGTYQLSP>FLLPQSPK---NRSTETNHQMKQGT

Parental  LSSPVRQESTVKDRDGFMVLLSKIEISSEKTMEIMKNLSSIQALEGNRQLEDLIGVSLVPCSLKSEARKT
          ...PVRQESTVKD.DGFMVLLSKIEISSEKTMEIMKNLSSIQ.LEGNRQLEDLIGVSLVPCSLK.EARK.
Retrocopy *A-PVRQESTVKDSDGFMVLLSKIEISSEKTMEIMKNLSSIQTLEGNRQLEDLIGVSLVPCSLKREARKA

Parental  KELMTKVIKQKLFEKKKSRITPKDHHLDSFEFLKAILN
          KELMTKVIKQKLFEKKK.RITPKDHH.DSFEFLKAILN
Retrocopy KELMTKVIKQKLFEKKK*RITPKDHHVDSFEFLKAILN

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	2.78 RPM
SRP007412_cerebellum	0.00 RPM	2.08 RPM
SRP007412_heart	0.00 RPM	1.59 RPM
SRP007412_kidney	0.04 RPM	2.66 RPM
SRP007412_liver	0.00 RPM	1.15 RPM
SRP007412_testis	0.00 RPM	31.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1547 was not detected

EST

No EST(s) were mapped for retro_mmus_1547 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_50533	382 libraries	407 libraries	262 libraries	15 libraries	6 libraries

The graphical summary, for retro_mmus_1547 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_1547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1547 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030710	1 retrocopy	retro_btau_747,
Callithrix jacchus	ENSCJAG00000016555	3 retrocopies	retro_cjac_2618, retro_cjac_3850, retro_cjac_3991,
Mus musculus	ENSMUSG00000028549	1 retrocopy	retro_mmus_1547 ,
Rattus norvegicus	ENSRNOG00000009116	1 retrocopy	retro_rnor_1472,
Tursiops truncatus	ENSTTRG00000007480	1 retrocopy	retro_ttru_996,