RetrogeneDB ID: retro_btau_873

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:70586567..70587039(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSBTAG00000004996
• Aliases: FAM206A, C8H9orf6, C9orf6
• Description: Protein FAM206A [Source:UniProtKB/Swiss-Prot;Acc:Q29S16]

Sequence

>retro_btau_873
AAACAGGATGTCAAAGGAAAACCCTGCGAGGACCACTGTATACTATAGCACTCTAACCGAATACATGTCATCATGTTGGC
GGGGTCTCATTCAGTTCTTCAAAGTGGAAAAAACAATTAAAAGAATTTTTAAATCAAATCAGTACCAACTGTTGCAGCCT
TCAGAACAAAGTCTCTGAGAAATTTAAGCGGGGGACACAGTTTCTCACAGAACTTGCACCTCTGTGTAAGATTTACTGCT
CAGGTGGAGAAGAATATATCATATCTAACTGTGTTAGAGGGTGGTTGATGAAAGTGAATGTAAACATTATCCATAAACCA
TCTATTCTTCAAGAGAAGCCATCCACCGAAGGCTACATTACAGTTGTGCTGTCCAAATTTGAAGAAATAAAAGCGAAACA
GGAGGGTTACTGACCCAAGAAGAATATGAAGAAATTATAGTGAAATGCATGAAAGCCACAGCAGCTACCTCA

Alignment

ORF - retro_btau_873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.12 %
• Parental protein coverage: 83.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KADVKGKPCEDHCILQHSNRICVITLAGSHPVLQSGK-TIKSISY-QISTNCSRLQNKVSGKFKRGAQFL
          K.DVKGKPCEDHCIL.HSNRI.VI.LAGSH.VLQSGK.TIK.I...QISTNC..LQNKVS.KFKRG.QFL
Retrocopy KQDVKGKPCEDHCIL*HSNRIHVIMLAGSHSVLQSGK>TIKRIFK>QISTNCCSLQNKVSEKFKRGTQFL

Parental  TELAPLCKIYCSDGEEYTISSCVRGRLMEVNENILHKPSILQEKPSTEGYIAVVLPKFEE-SKSITEGLL
          TELAPLCKIYCS.GEEY.IS.CVRG.LM.VN.NI.HKPSILQEKPSTEGYI.VVL.KFEE..KS.T.GLL
Retrocopy TELAPLCKIYCSGGEEYIISNCVRGWLMKVNVNIIHKPSILQEKPSTEGYITVVLSKFEE<NKSETGGLL

Parental  TQKEYEEVVVKRLRATTAAS
          TQ.EYEE..VK...AT.A.S
Retrocopy TQEEYEEIIVKCMKATAATS

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	9.44 RPM
ERP005899_muscle	0.00 RPM	7.71 RPM
SRP017611_brain	0.00 RPM	11.60 RPM
SRP017611_kidney	0.00 RPM	16.30 RPM
SRP017611_liver	0.00 RPM	6.12 RPM
SRP030211_testis	0.00 RPM	18.29 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_873 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873 ,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583,