RetrogeneDB ID: retro_btau_1237

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:99934683..99935227(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NACA
• Ensembl ID: ENSBTAG00000010701
• Aliases: None
• Description: Nascent polypeptide-associated complex subunit alpha [Source:UniProtKB/Swiss-Prot;Acc:Q5E9A1]

Sequence

>retro_btau_1237
GAACAGAAACCAGAACTTGAGGAACAGGATTCTGTGCAAGCAACCACACAAGCCCGGCTGGCAGCAGCAGCTGAAACTGA
TGAAGAACCAGTTAGGAAAGCAAAACAGAGCTGGAGTGAAAGGAAGGCGTGGAAGGCTATGTCCAAACTAGGTCTTCACC
AGGTTACAGGGGTTACTAGAGTGGCTATCCAGACATCTAAGAATATCCTTTTTGTCATCAAGAAACCAGATGTGTACAAG
AGCCCAGCTTCAAATACCTAGATAGTTTTGAGGGAAGCCAAGATCAAGGACTTATCTCAGCAAGTACAATTAGCAGCTGC
TGAGAAATTCAACGTTCAAAGTGAAGCTGTTTCCAAAATTCAGGAAAACACAGATTCCAACTGTACAAGAGGAGAGTGAA
GAGGAAGAGGTTGATGAAACAGGTGTGGAAGTTAAGGGGCTAGAATCGGTCACGTCACAAGCAAATGTGTCAAGAACAAA
GGCAGTCCGAGCCCTGAAGAACAACAGTAATGATATTGTAAGTGCTATTACGGCATTAACAATA

Alignment

ORF - retro_btau_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.63 %
• Parental protein coverage: 85.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESVPELEEQDSTQATTQQAQLAAAAEIDEEPVSKAKQSRSEKKARKAMSKLGLRQVTGVTRVTIRKSKNI
          E..PELEEQDS.QATTQ.A.LAAAAE.DEEPV.KAKQS.SE.KA.KAMSKLGL.QVTGVTRV.I..SKNI
Retrocopy EQKPELEEQDSVQATTQ-ARLAAAAETDEEPVRKAKQSWSERKAWKAMSKLGLHQVTGVTRVAIQTSKNI

Parental  LFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQLAAAEKFKVQGEAVSNIQENTQT-PTVQEESEEEEV
          LFVI.KPDVYKSPAS.T.IV..EAKI.DLSQQ.QLAAAEKF.VQ.EAVS.IQENT.......E..E.EEV
Retrocopy LFVIKKPDVYKSPASNT*IVLREAKIKDLSQQVQLAAAEKFNVQSEAVSKIQENTDS>TVQEESEE-EEV

Parental  DETGVEVKDIELVMSQANVSRAKAVRALKNNSNDIVNAIMELTM
          DETGVEVK..E.V.SQANVSR.KAVRALKNNSNDIV.AI..LT.
Retrocopy DETGVEVKGLESVTSQANVSRTKAVRALKNNSNDIVSAITALTI

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	127.32 RPM
ERP005899_muscle	0.00 RPM	381.35 RPM
SRP017611_brain	0.00 RPM	75.37 RPM
SRP017611_kidney	0.00 RPM	139.29 RPM
SRP017611_liver	0.00 RPM	90.23 RPM
SRP030211_testis	0.00 RPM	175.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1237 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1237 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004175	3 retrocopies	retro_amel_1725, retro_amel_1821, retro_amel_643,
Bos taurus	ENSBTAG00000010701	2 retrocopies	retro_btau_1237 , retro_btau_1620,
Canis familiaris	ENSCAFG00000000141	8 retrocopies	retro_cfam_1502, retro_cfam_1561, retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus	ENSCJAG00000010701	8 retrocopies	retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Erinaceus europaeus	ENSEEUG00000010458	5 retrocopies	retro_eeur_170, retro_eeur_207, retro_eeur_242, retro_eeur_334, retro_eeur_520,
Loxodonta africana	ENSLAFG00000004598	6 retrocopies	retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491, retro_lafr_958,
Myotis lucifugus	ENSMLUG00000001169	16 retrocopies	retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Nomascus leucogenys	ENSNLEG00000017449	7 retrocopies	retro_nleu_1358, retro_nleu_20, retro_nleu_2522, retro_nleu_478, retro_nleu_754, retro_nleu_839, retro_nleu_941,
Pongo abelii	ENSPPYG00000004670	6 retrocopies	retro_pabe_2507, retro_pabe_26, retro_pabe_3279, retro_pabe_633, retro_pabe_656, retro_pabe_764,
Sarcophilus harrisii	ENSSHAG00000002175	1 retrocopy	retro_shar_213,
Ictidomys tridecemlineatus	ENSSTOG00000009028	1 retrocopy	retro_itri_367,
Vicugna pacos	ENSVPAG00000004028	2 retrocopies	retro_vpac_485, retro_vpac_611,