RetrogeneDB ID: retro_btau_1161

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:29218578..29219021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTF3
• Ensembl ID: ENSBTAG00000010012
• Aliases: None
• Description: transcription factor BTF3 [Source:RefSeq peptide;Acc:NP_001020485]

Sequence

>retro_btau_1161
AAGTTGCCCACACAAGTGTGCACTGGTGGGAAAGGAACTGCTTGCAGAAAGAAGAAGGTGGTTCATAGAACAACCACGGC
TGATGACAAAAAACTTCAGTTCTCTTTAAAGAAGTTAGGGTTAGACATTATCCCTGGTATTGAAGAGGCGAGTAGGTTCA
CAAATCAAGGAACACTGATCCACTTCAACAACGCTAACGTTCAGGCATCTCTGGCAGCAAACACTTCCACCGTTACAGGC
AATGCTGAGACACAGCAGCTGACAGAAATGCTACCCAGCATCTTAAACCAGCTTGGTGCGGATAGTATGACTGGTTTGAG
GAGACTCGTCAAGCTCTGCCCAAACAATCTGTGTACGGAGGAGCACCACTTGCCAGAGAAGAAAATGATGAAGGTACAGA
TCTAGTGGATAATTTTGACGAGGCTTCCAAGAATGCAGCAAAC

Alignment

ORF - retro_btau_1161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.16 %
• Parental protein coverage: 92.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIEEVNMFTNQGTVIHFNNPKVQAS
          KL..QV..GGKGTA.RKKKVVHRT.TADDKKLQFSLKKLG...I.GIEE...FTNQGT.IHFNN..VQAS
Retrocopy KLPTQVCTGGKGTACRKKKVVHRTTTADDKKLQFSLKKLGLDIIPGIEEASRFTNQGTLIHFNNANVQAS

Parental  LAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLA-EALPKQSVDGKAPLATGEEDDDEVPDLVE
          LAANT.T.TG.AET.QLTEMLPSILNQLGADS.T.LRRL...ALPKQSV.G.APLA...E..DE..DLV.
Retrocopy LAANTSTVTGNAETQQLTEMLPSILNQLGADSMTGLRRLV<QALPKQSVYGGAPLA--REENDEGTDLVD

Parental  NFDEASKNEAN
          NFDEASKN.AN
Retrocopy NFDEASKNAAN

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	0.65 RPM	108.29 RPM
ERP005899_muscle	0.05 RPM	192.26 RPM
SRP017611_brain	0.14 RPM	64.77 RPM
SRP017611_kidney	0.24 RPM	149.96 RPM
SRP017611_liver	0.00 RPM	80.34 RPM
SRP030211_testis	0.01 RPM	131.56 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1161 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1161 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1161 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011563	14 retrocopies	retro_amel_1257, retro_amel_1279, retro_amel_1324, retro_amel_1334, retro_amel_1433, retro_amel_166, retro_amel_1769, retro_amel_182, retro_amel_1841, retro_amel_480, retro_amel_513, retro_amel_784, retro_amel_908, retro_amel_986,
Bos taurus	ENSBTAG00000010012	5 retrocopies	retro_btau_1161 , retro_btau_1344, retro_btau_1361, retro_btau_459, retro_btau_551,
Bos taurus	ENSBTAG00000011025	1 retrocopy	retro_btau_1030,
Canis familiaris	ENSCAFG00000008212	3 retrocopies	retro_cfam_1660, retro_cfam_1741, retro_cfam_531,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Cavia porcellus	ENSCPOG00000012832	1 retrocopy	retro_cpor_81,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Equus caballus	ENSECAG00000021629	1 retrocopy	retro_ecab_200,
Echinops telfairi	ENSETEG00000017341	5 retrocopies	retro_etel_1216, retro_etel_1394, retro_etel_1997, retro_etel_405, retro_etel_960,
Felis catus	ENSFCAG00000023973	10 retrocopies	retro_fcat_1044, retro_fcat_1378, retro_fcat_1438, retro_fcat_187, retro_fcat_188, retro_fcat_225, retro_fcat_28, retro_fcat_419, retro_fcat_593, retro_fcat_919,
Gorilla gorilla	ENSGGOG00000000166	10 retrocopies	retro_ggor_1082, retro_ggor_1682, retro_ggor_1961, retro_ggor_2054, retro_ggor_2399, retro_ggor_2647, retro_ggor_2667, retro_ggor_548, retro_ggor_81, retro_ggor_946,
Myotis lucifugus	ENSMLUG00000012912	11 retrocopies	retro_mluc_1024, retro_mluc_1349, retro_mluc_1459, retro_mluc_1748, retro_mluc_1820, retro_mluc_1823, retro_mluc_2560, retro_mluc_2602, retro_mluc_482, retro_mluc_682, retro_mluc_694,
Macaca mulatta	ENSMMUG00000022291	2 retrocopies	retro_mmul_105, retro_mmul_2424,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Otolemur garnettii	ENSOGAG00000013918	1 retrocopy	retro_ogar_46,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956, retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Rattus norvegicus	ENSRNOG00000016912	9 retrocopies	retro_rnor_187, retro_rnor_194, retro_rnor_2121, retro_rnor_2520, retro_rnor_2990, retro_rnor_2991, retro_rnor_2999, retro_rnor_836, retro_rnor_953,