RetrogeneDB ID: retro_btau_609

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:70318718..70319018(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96B
• Ensembl ID: ENSBTAG00000013931
• Aliases: None
• Description: mitotic spindle-associated MMXD complex subunit MIP18 [Source:RefSeq peptide;Acc:NP_001179967]

Sequence

>retro_btau_609
ATCTTCAATCTGATTAGTTCTATCAATGATCCAGGGCACCCACTGATGTTAGAGGAATTTAACACAGTAGAGCAAGTCTA
CATTCAGGCAAGAAACCCCGAGAGAACAGTGGCCATGGCATTCACAATCATTGTTCTGCACTGCAGCATGGCCACCATTA
TTGGCCAGTCATGCTTCATTCATTCATTTCCTCAGCATTTCAGGATGGACATGCACATTATAACAGGGACTCGTGACTCA
AAGCATGCAGTGAACAAGCCCCCCGGGAATAATGAACAGATAGCAGCTGCCCTAGGGAAC

Alignment

ORF - retro_btau_609 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.25 %
• Parental protein coverage: 63.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IFDLIRSINDPEHPLTLEELNVVEQVRVQVSDPESTVAVAFTPTIPHCSMATLIGLSIKVKLLRSLPQRF
          IF.LI.SINDP.HPL.LEE.N.VEQV..Q...PE.TVA.AFT....HCSMAT.IG.S.......S.PQ.F
Retrocopy IFNLISSINDPGHPLMLEEFNTVEQVYIQARNPERTVAMAFTIIVLHCSMATIIGQSC---FIHSFPQHF

Parental  KMDVHITPGTHASEHAVNKQLADKERVAAALEN
          .MD.HI..GT..S.HAVNK.....E..AAAL.N
Retrocopy RMDMHIITGTRDSKHAVNKPPGNNEQIAAALGN

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
ERP005899_liver	0.00 RPM	5.62 RPM
ERP005899_muscle	0.00 RPM	26.13 RPM
SRP017611_brain	0.00 RPM	12.38 RPM
SRP017611_kidney	0.00 RPM	19.92 RPM
SRP017611_liver	0.00 RPM	9.51 RPM
SRP030211_testis	0.00 RPM	23.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_609 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017164	1 retrocopy	retro_amel_1340,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Bos taurus	ENSBTAG00000013931	1 retrocopy	retro_btau_609 ,
Canis familiaris	ENSCAFG00000020394	2 retrocopies	retro_cfam_479, retro_cfam_802,
Felis catus	ENSFCAG00000029216	2 retrocopies	retro_fcat_1464, retro_fcat_697,
Mustela putorius furo	ENSMPUG00000005303	2 retrocopies	retro_mputfur_1547, retro_mputfur_302,
Mus musculus	ENSMUSG00000031879	1 retrocopy	retro_mmus_2927,
Sarcophilus harrisii	ENSSHAG00000004698	1 retrocopy	retro_shar_590,
Tarsius syrichta	ENSTSYG00000005006	2 retrocopies	retro_tsyr_1305, retro_tsyr_149,