RetrogeneDB ID: retro_btau_1835

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:90638549..90639115(-)
• Located in intron of: ENSBTAG00000005124

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.87535
• Ensembl ID: ENSBTAG00000005744
• Aliases: None
• Description: 4-hydroxybenzoate polyprenyltransferase, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001039358]

Sequence

>retro_btau_1835
GCTCTTGAAGCAGCATCCCTACTTCTTGTCATCACCTACCCACTAAAGAAAGGAATTACATACTGGCCTCAGTTGGCCTT
GGAATTGACATTTAATTGAGGAGCATTACTTGTGTGGTCTGCTATCAAGGGTTCCTGTGATCCATCTGTTTGCCTTCCTC
TTTATTTTTCTGGAATTATGTGGACTCTAATATACGATACTATCTATGCCCATCAGAATAAGAGAGATGATGCTTTGATC
GGGCTTAAGTCCACGGCACTGCAGTTCTGGGAAGACACCAAGAAGTGGCTCAGCGGTTTCAGTGTGGCCTGCTGGGGGCG
CTGAGTCTGGTGGGAGTGAAGAGCGGCCAGACTGCACCCTACTACACTCCCCTGGCTGCTATAGGAGCCCATGTGGCTCA
CCAGATTTATACTCTGGACATCCACAGACCTGAAGACTGTTGGGAAAAGTTCACCTCCAACCAAACAACAGAATTAATAA
TTTTTTAAGGGACTGTCCTTAGGAATTTGTGGAAAGCAAAGGAGACCAATGAAACAAAGAAAAATATAGAAAACAGAATA
GAAAAT

Alignment

ORF - retro_btau_1835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 50.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALGAASLLLVTTYPLMKRITYWPQLALGLTFNWGALLGWSAVKGSCDPSVCLPLYFSGIMWTLIYDTIYA
          AL.AASLLLV.TYPL.K.ITYWPQLAL.LTFN.GALL.WSA.KGSCDPSVCLPLYFSGIMWTLIYDTIYA
Retrocopy ALEAASLLLVITYPLKKGITYWPQLALELTFN*GALLVWSAIKGSCDPSVCLPLYFSGIMWTLIYDTIYA

Parental  HQDKKDDALIGLKSTALLFREDTKKWLSGFSVA-MLGALSLVGVNSGQTMPYYTALAAVGAHLAHQIYTL
          HQ.K.DDALIGLKSTAL.F.EDTKKWLSGFSVA..LGALSLVGV.SGQT.PYYT.LAA.GAH.AHQIYTL
Retrocopy HQNKRDDALIGLKSTALQFWEDTKKWLSGFSVA<LLGALSLVGVKSGQTAPYYTPLAAIGAHVAHQIYTL

Parental  DIHRPEDCWEKFTSNRTIGLIIFLGIVLGNLCKAKETDKTRKNIENRMEN
          DIHRPEDCWEKFTSN.T..LIIF.G.VL.NL.KAKET..T.KNIENR.EN
Retrocopy DIHRPEDCWEKFTSNQTTELIIF*GTVLRNLWKAKETNETKKNIENRIEN

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	0.07 RPM	62.58 RPM
ERP005899_muscle	0.00 RPM	40.49 RPM
SRP017611_brain	0.00 RPM	7.90 RPM
SRP017611_kidney	0.00 RPM	42.20 RPM
SRP017611_liver	0.00 RPM	21.60 RPM
SRP030211_testis	0.02 RPM	10.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1835 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005006	1 retrocopy	retro_amel_1898,
Bos taurus	ENSBTAG00000005744	1 retrocopy	retro_btau_1835 ,
Cavia porcellus	ENSCPOG00000011458	1 retrocopy	retro_cpor_1202,
Equus caballus	ENSECAG00000012542	1 retrocopy	retro_ecab_432,
Myotis lucifugus	ENSMLUG00000015267	1 retrocopy	retro_mluc_1776,
Mus musculus	ENSMUSG00000029319	1 retrocopy	retro_mmus_2883,
Tarsius syrichta	ENSTSYG00000013801	30 retrocopies	retro_tsyr_1015, retro_tsyr_1155, retro_tsyr_1173, retro_tsyr_1180, retro_tsyr_1207, retro_tsyr_1235, retro_tsyr_1327, retro_tsyr_1335, retro_tsyr_1385, retro_tsyr_1451, retro_tsyr_1491, retro_tsyr_1646, retro_tsyr_1709, retro_tsyr_1742, retro_tsyr_2015, retro_tsyr_2062, retro_tsyr_2087, retro_tsyr_2136, retro_tsyr_2146, retro_tsyr_466, retro_tsyr_513, retro_tsyr_533, retro_tsyr_54, retro_tsyr_548, retro_tsyr_607, retro_tsyr_619, retro_tsyr_654, retro_tsyr_776, retro_tsyr_839, retro_tsyr_995,
Tursiops truncatus	ENSTTRG00000005647	1 retrocopy	retro_ttru_1726,