RetrogeneDB ID: retro_mmus_1618

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:14881389..14881752(-)
• Located in intron of: ENSMUSG00000046991

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem126b
• Ensembl ID: ENSMUSG00000030614
• Aliases: None
• Description: transmembrane protein 126B [Source:MGI Symbol;Acc:MGI:1915722]

Sequence

>retro_mmus_1618
AGTGTCTCTGGAATACAGCCAAACTAGTTTCAAAACAATGGCAAACTTTACTAGGAAGCTTTGAAGACTTATGCATCATT
GACTATACTTTTGTTTGAGGTTACCATCATTTCTTACAAGCCCTTTGTGATTGACACTTTGCATTCAAGTAACATAAGCA
AAGAAAAGTGTTTTTCTGAGACGGTCCCTGGTTGACTTCCTATGTGGTGTTTTATATCCTAGCGCTGTGGCTTTTTACAG
AAACGAGTGTTTGGCAGTTAAGCAGCACAGGATCCCACTGTCACAGAAAGGAAGGGATCCAGCGCATTGGTTGTTCTTTT
ATCACGTTAGAATGGAGTGATGGTCATTGTTCTGCTTTTCAGA

Alignment

ORF - retro_mmus_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.42 %
• Parental protein coverage: 53.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLSGIMANLVFRNSFKVKYEALKTYASLTTLPVLATIVSYKLFVTDALQSGDISKESC-VLRSALIGMAC
          S.SGI..N..F.N..K...EALKTYASLT.L....TI.SYK.FV.D.L.S..ISKE.C..LR..L....C
Retrocopy SVSGIQPN*-FQNNGKLY*EALKTYASLTILLFEVTIISYKPFVIDTLHSSNISKEKC>FLRRSLVDFLC

Parental  GVSYPSALAFYKNGRLAVKYQTVPLPPKGRVMLHWLLLCQTGMK-AMAIPLFFQ
          GV.YPSA.AFY.N..LAVK....PL..KGR...HWL......M...M.I.L.F.
Retrocopy GVLYPSAVAFYRNECLAVKQHRIPLSQKGRDPAHWLFFYHVRME<VMVIVLLFR

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	21.73 RPM
SRP007412_cerebellum	0.00 RPM	18.32 RPM
SRP007412_heart	0.00 RPM	19.27 RPM
SRP007412_kidney	0.00 RPM	24.52 RPM
SRP007412_liver	0.00 RPM	12.59 RPM
SRP007412_testis	0.00 RPM	3.02 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1618 was not detected

EST

No EST(s) were mapped for retro_mmus_1618 retrocopy.

TSS

No TSS is located nearby retro_mmus_1618 retrocopy 5' end.

Lab

retro_mmus_1618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1618 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
Bos taurus	ENSBTAG00000020596	1 retrocopy	retro_btau_420,
Echinops telfairi	ENSETEG00000008939	1 retrocopy	retro_etel_200,
Mus musculus	ENSMUSG00000030614	1 retrocopy	retro_mmus_1618 ,
Mus musculus	ENSMUSG00000030615	3 retrocopies	retro_mmus_1431, retro_mmus_1531, retro_mmus_3555,
Oryctolagus cuniculus	ENSOCUG00000016529	3 retrocopies	retro_ocun_1656, retro_ocun_1671, retro_ocun_607,
Sus scrofa	ENSSSCG00000014905	1 retrocopy	retro_sscr_452,