RetrogeneDB ID: retro_btau_1022

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:27327860..27328376(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.79452
• Ensembl ID: ENSBTAG00000018496
• Aliases: None
• Description: mitochondrial import inner membrane translocase subunit Tim17-B [Source:RefSeq peptide;Acc:NP_001039953]

Sequence

>retro_btau_1022
GAGCCTTGCCCATGGAGAATTGTGGATGATTGCGGTGGAACCTTCATTATGGGCGTTAGCTGCGATACAGTCTTCCAGGC
CATGAAGGGTTTCTGCAATGACCCTGTAGAAATTCGGCGCTGATTGAGAGGCAGTGTCAATGCTGTTAAAGAACAAAGCC
CCTCAGACTGGAGGTAGCTTCGAGGTGTGTGGGCAGGAGTGGGGAGGCTGTTTTCCACCATCCACGGGTCTGGTGTGGCT
GCGGGGCAAGGAAGATTTCTGGTACTCTATTACCAGTGAAGCACTGACAGGTCTGTGCTAGCTGCCCACAGTGGCTCATT
GGTGATGGTGGGCTCAGCAATGCTTGGGGGGGGGGTGGGCATTCTGTTGGCCCTCATCCAGCGTGTTGGCGTCCTCCACA
CTCACTACACTATCCAGCACTTCCTCAGTGCACTCCCCTTATTGGAGAACCCCAACAAGCTGCCCCCAAAGGAGGGTACC
AAGGCCCGAGGCTACCCCAGCTATCAGCAATATCAC

Alignment

ORF - retro_btau_1022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.14 %
• Parental protein coverage: 96.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPCPWRIVDDCGGAFTMGVIGGGVFQAIKGFRNAPVGMRHRLRGSVNAV-RIRAPQIGGSFAV----WGG
          EPCPWRIVDDCGG.F.MGV....VFQA.KGF.N.PV..R..LRGSVNAV....APQ.GGSF.V....WGG
Retrocopy EPCPWRIVDDCGGTFIMGVSCDTVFQAMKGFCNDPVEIRR*LRGSVNAV>KNKAPQTGGSFEVCGQEWGG

Parental  LFSTIDCGLVRLRGKEDPWNSITSGALTG-AVLAARSGPLAMVGSAMM---GGILLALIEGVGILLTRYT
          .F.....GLV.LRGKED.W.SITS.ALTG..VLAA.SG.L.MVGSAM.....GILLALI..VG.L.T.YT
Retrocopy CFPP-STGLVWLRGKEDFWYSITSEALTG<SVLAAHSGSLVMVGSAMLXXXXGILLALIQRVGVLHTHYT

Parental  AQQFRNAPPFLEDPGQLPSKEGTPGPGYPSYQQYH
          .Q.F..A.P.LE.P..LP.KEGT...GYPSYQQYH
Retrocopy IQHFLSALPLLENPNKLPPKEGTKARGYPSYQQYH

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	0.29 RPM	6.13 RPM
ERP005899_muscle	0.00 RPM	26.24 RPM
SRP017611_brain	0.00 RPM	11.05 RPM
SRP017611_kidney	0.12 RPM	23.00 RPM
SRP017611_liver	0.00 RPM	13.21 RPM
SRP030211_testis	0.09 RPM	11.50 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1022 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1022 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012474	1 retrocopy	retro_amel_717,
Bos taurus	ENSBTAG00000018496	4 retrocopies	retro_btau_1022 , retro_btau_1550, retro_btau_1552, retro_btau_882,
Bos taurus	ENSBTAG00000047059	3 retrocopies	retro_btau_1098, retro_btau_1590, retro_btau_872,
Cavia porcellus	ENSCPOG00000008768	2 retrocopies	retro_cpor_867, retro_cpor_893,
Dasypus novemcinctus	ENSDNOG00000025897	2 retrocopies	retro_dnov_2282, retro_dnov_2406,
Felis catus	ENSFCAG00000002569	2 retrocopies	retro_fcat_1429, retro_fcat_1654,
Gorilla gorilla	ENSGGOG00000011427	1 retrocopy	retro_ggor_779,
Macropus eugenii	ENSMEUG00000004174	1 retrocopy	retro_meug_2071,
Microcebus murinus	ENSMICG00000005971	3 retrocopies	retro_mmur_1128, retro_mmur_1272, retro_mmur_232,
Myotis lucifugus	ENSMLUG00000009148	1 retrocopy	retro_mluc_148,
Macaca mulatta	ENSMMUG00000004547	1 retrocopy	retro_mmul_796,
Mustela putorius furo	ENSMPUG00000013675	1 retrocopy	retro_mputfur_1232,
Mus musculus	ENSMUSG00000031158	1 retrocopy	retro_mmus_1509,
Nomascus leucogenys	ENSNLEG00000007902	1 retrocopy	retro_nleu_1616,
Oryctolagus cuniculus	ENSOCUG00000027418	2 retrocopies	retro_ocun_121, retro_ocun_1451,
Pteropus vampyrus	ENSPVAG00000007643	1 retrocopy	retro_pvam_470,
Ictidomys tridecemlineatus	ENSSTOG00000014173	1 retrocopy	retro_itri_83,
Tarsius syrichta	ENSTSYG00000010396	2 retrocopies	retro_tsyr_1132, retro_tsyr_1703,
Vicugna pacos	ENSVPAG00000009578	1 retrocopy	retro_vpac_92,