RetrogeneDB ID: retro_mmus_436

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:47915153..47915689(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Taf8
• Ensembl ID: ENSMUSG00000023980
• Aliases: Taf8, AW260255, Tbn
• Description: TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factorq [Source:MGI Symbol;Acc:MGI:1926879]

Sequence

>retro_mmus_436
TTAAGGGAAATGCTGTTTAGCTACATCTCAGAAATCCGGAGAGGTGCCAAGTCATACTGCGAACACACAGCCAGAACCAA
ACCCACACTGTTGGACATCGTGGTCACATTGGTTGAAATGGACTTCAGTGTTGACACGCTACCTGCTTATACAAAACGGG
CTCAGAGGATGGTCATCAATGAACCTCCAGTAACCAATCAGCCAGTGACACCCAAGGCCCTTACTGCAGGGCAGAACTGA
CCCCATCTGCCACCCATCCCCAGCCATTTTCCTGAGTTTCGGGATCCCCACACCTACAACAAAACTCCAACATACCATGA
GCCAGTCTCTGAGCACCAGGTCATTCGGGAGAAGGCCTTATCTCAAAGGTGAGATAAAGTGGAGTGAGTACTCACATGCT
ACATGGCCAAGACAGGAGAGACCCAGAGTCTTTTCAAGGATGATGCCAGCACTTTCCCCTGGATTGCTGCCAAACCTTCA
CCATCCCCTACCTCACGGCCTTGCTTCTCTCCAAGCTGGAGAAACAGCTGATGGAA

Alignment

ORF - retro_mmus_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTEMLQSYISEIGRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVDTLPAYAKRSQRMVITAPPVTNQPVT
          L.EML.SYISEI.R.AKSYCEHTART.PTL.DIVVTLVEM.F.VDTLPAY.KR.QRMVI..PPVTNQPVT
Retrocopy LREMLFSYISEIRRGAKSYCEHTARTKPTLLDIVVTLVEMDFSVDTLPAYTKRAQRMVINEPPVTNQPVT

Parental  PKALTAGQNRPHPPHIPSHFPEFPDPHTYIKTPTYREPVSDYQILREKAASQRRD-VERALTRFMAKTGE
          PKALTAGQN.PH.P.IPSHFPEF.DPHTY.KTPTY.EPVS..Q..REKA.SQR.D.VE..LT..MAKTGE
Retrocopy PKALTAGQN*PHLPPIPSHFPEFRDPHTYNKTPTYHEPVSEHQVIREKALSQR*DKVE*VLTCYMAKTGE

Parental  TQSLFKDDVSTFPLIAARP-FTIPYLTALLPSELEIQQME
          TQSLFKDD.STFP.IAA.P.FTIPYLTALL.S.LE.Q.ME
Retrocopy TQSLFKDDASTFPWIAAKP<FTIPYLTALLLSKLEKQLME

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	13.29 RPM
SRP007412_cerebellum	0.00 RPM	17.33 RPM
SRP007412_heart	0.00 RPM	13.01 RPM
SRP007412_kidney	0.00 RPM	17.86 RPM
SRP007412_liver	0.00 RPM	10.43 RPM
SRP007412_testis	0.00 RPM	7.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_436 was not detected

EST

No EST(s) were mapped for retro_mmus_436 retrocopy.

TSS

No TSS is located nearby retro_mmus_436 retrocopy 5' end.

Lab

retro_mmus_436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010516	1 retrocopy	retro_chof_661,
Macropus eugenii	ENSMEUG00000006952	1 retrocopy	retro_meug_150,
Microcebus murinus	ENSMICG00000011353	6 retrocopies	retro_mmur_112, retro_mmur_1455, retro_mmur_443, retro_mmur_455, retro_mmur_554, retro_mmur_555,
Monodelphis domestica	ENSMODG00000012785	2 retrocopies	retro_mdom_1206, retro_mdom_1357,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436 ,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317,