RetrogeneDB ID: retro_btau_648

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:52113135..52113594(-)
• Located in intron of: ENSBTAG00000000215

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCU
• Ensembl ID: ENSBTAG00000011787
• Aliases: None
• Description: iron-sulfur cluster assembly enzyme ISCU, mitochondrial [Source:RefSeq peptide;Acc:NP_001069151]

Sequence

>retro_btau_648
GCAGCCCTGCTGCTGCTCCAGCCCCTCGCCTACCTGCCTGCCCCCTGGGAGCTGTCAGCTATGGCTTGGCATTCACACGA
GACTGCAGTTGATTCTTATGAAAATCCCTGAAACCTGGGGTCCCCTGGCAAGGCATCTACAAATGTTGGAACTGGATAGG
TGGGGGCTCCAGCGTGTAGTGATGAAATGAAAATACAGATTAAAGTGGGTGAAAAGAGAAAGATGGTGAACACCAGTTTT
AAAATATTTGGCTGTGGTTCTGCCACTCCCAGCAGCTGGTCAGCCCCTGAATGGGTGAAGGGGAAGATGGTGGAGGACGC
CTCGACCATGAAGAACACAGATACCGCCAAGGAACTCTGCCTTCTCCCTGTGAAACTGCACTACTCCACATTGGCCAGAG
AGGCCATCAAGGCCGCCCTGGCTGACTACAAACTCAAACAAGAAAGAAGAGGACAAGAA

Alignment

ORF - retro_btau_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.05 %
• Parental protein coverage: 91.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASAVLLRAPRLPAR-ELSAPARLYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVD
          AA...L.....LPA..ELSA.A...H...VD.YENP.N.GS..K.S.NVGTG.VGAPAC.D.MK.QI.V.
Retrocopy AALLLLQPLAYLPAPWELSAMAWHSHETAVDSYENP*NLGSPGKASTNVGTG*VGAPACSDEMKIQIKVG

Parental  EKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAAL
          EK.K.V...FK.FGCGSA..SS..A.EWVKGK.VE.A.T.KNTD.AKELCL.PVKLH.S.LA..AIKAAL
Retrocopy EKRKMVNTSFKIFGCGSATPSSWSAPEWVKGKMVEDASTMKNTDTAKELCLLPVKLHYSTLAREAIKAAL

Parental  ADYKLKQEPKTGE
          ADYKLKQE....E
Retrocopy ADYKLKQERRGQE

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	45.71 RPM
ERP005899_muscle	0.16 RPM	34.74 RPM
SRP017611_brain	0.00 RPM	72.26 RPM
SRP017611_kidney	0.12 RPM	111.02 RPM
SRP017611_liver	0.08 RPM	35.04 RPM
SRP030211_testis	0.18 RPM	103.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_648 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016405	3 retrocopies	retro_amel_1338, retro_amel_755, retro_amel_902,
Bos taurus	ENSBTAG00000011787	3 retrocopies	retro_btau_378, retro_btau_646, retro_btau_648 ,
Canis familiaris	ENSCAFG00000011324	4 retrocopies	retro_cfam_388, retro_cfam_390, retro_cfam_599, retro_cfam_686,
Choloepus hoffmanni	ENSCHOG00000011773	2 retrocopies	retro_chof_229, retro_chof_2698,
Callithrix jacchus	ENSCJAG00000015374	2 retrocopies	retro_cjac_1584, retro_cjac_1644,
Cavia porcellus	ENSCPOG00000010986	1 retrocopy	retro_cpor_1201,
Equus caballus	ENSECAG00000019879	3 retrocopies	retro_ecab_359, retro_ecab_753, retro_ecab_849,
Felis catus	ENSFCAG00000014044	2 retrocopies	retro_fcat_1769, retro_fcat_471,
Homo sapiens	ENSG00000136003	2 retrocopies	retro_hsap_3596, retro_hsap_468,
Gorilla gorilla	ENSGGOG00000011579	2 retrocopies	retro_ggor_2426, retro_ggor_446,
Loxodonta africana	ENSLAFG00000007170	2 retrocopies	retro_lafr_609, retro_lafr_728,
Microcebus murinus	ENSMICG00000013067	4 retrocopies	retro_mmur_1359, retro_mmur_558, retro_mmur_636, retro_mmur_81,
Macaca mulatta	ENSMMUG00000017126	1 retrocopy	retro_mmul_572,
Monodelphis domestica	ENSMODG00000002828	1 retrocopy	retro_mdom_1924,
Mus musculus	ENSMUSG00000025825	2 retrocopies	retro_mmus_1806, retro_mmus_3317,
Nomascus leucogenys	ENSNLEG00000006797	2 retrocopies	retro_nleu_299, retro_nleu_884,
Oryctolagus cuniculus	ENSOCUG00000016305	1 retrocopy	retro_ocun_637,
Procavia capensis	ENSPCAG00000007604	2 retrocopies	retro_pcap_257, retro_pcap_86,
Pongo abelii	ENSPPYG00000004920	3 retrocopies	retro_pabe_1753, retro_pabe_266, retro_pabe_2956,
Tupaia belangeri	ENSTBEG00000001086	3 retrocopies	retro_tbel_1987, retro_tbel_2588, retro_tbel_545,
Tarsius syrichta	ENSTSYG00000013952	2 retrocopies	retro_tsyr_1484, retro_tsyr_98,
Tursiops truncatus	ENSTTRG00000004036	1 retrocopy	retro_ttru_1720,
Xenopus tropicalis	ENSXETG00000027428	1 retrocopy	retro_xtro_66,