RetrogeneDB ID: retro_btau_1173

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:18382769..18383219(+)
• Located in intron of: ENSBTAG00000020268

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2N
• Ensembl ID: ENSBTAG00000021767
• Aliases: None
• Description: Ubiquitin-conjugating enzyme E2 N [Source:UniProtKB/Swiss-Prot;Acc:Q0P5K3]

Sequence

>retro_btau_1173
ATGGCCGGGCTGCCCCACAGGATTATTAAGGAAACCCAGCGTTTGCTGGCAGAACCAGTTCCCGGCGTTAAAGCAAAACC
AGATGAGAGCAACGCCCGTTATTTTCATGTGGTCATTGCCAGCCCTCAGGATTCCCCCTTTGAGGGAGGAGTTTTTAAGC
TTGAACTATTCCTTCCAGAATACCCAATGGCAGCCCTTAAAGTACATTTCATGACCAAAATTTATCATCCTAATGTAGAC
AAGTTGGGAAGAATATGTTTAGATATTTTGAAAGATAAGTGGTCCCCGTCACTGCAGATTTGCACAGTTCTGCTATCGAT
CTAGGCTTTGTTAAGTGCTCCCATTCCAGATGATCCATTAGCAAATGATGTAGCAGAGCAGTGGAAGACCAACGAAGCCC
AAGCCCTAGAAACAGCTAGAGCATGGACCAGGCTATATGCCATGAATAAT

Alignment

ORF - retro_btau_1173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.39 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVR
          MAGLP.RIIKETQRLLAEPVPG.KA.PDESNARYFHVVIA.PQDSPFEGG.FKLELFLPE.YPMAA.KV.
Retrocopy MAGLPHRIIKETQRLLAEPVPGVKAKPDESNARYFHVVIASPQDSPFEGGVFKLELFLPE-YPMAALKVH

Parental  FMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETA
          FMTKIYHPNVDKLGRICLDILKDKWSP.LQI.TVLLSI.ALLSAP.PDDPLANDVAEQWKTNEAQA.ETA
Retrocopy FMTKIYHPNVDKLGRICLDILKDKWSPSLQICTVLLSI*ALLSAPIPDDPLANDVAEQWKTNEAQALETA

Parental  RAWTRLYAMNN
          RAWTRLYAMNN
Retrocopy RAWTRLYAMNN

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	0.36 RPM	36.99 RPM
ERP005899_muscle	0.21 RPM	57.54 RPM
SRP017611_brain	0.00 RPM	62.08 RPM
SRP017611_kidney	0.41 RPM	60.63 RPM
SRP017611_liver	0.08 RPM	23.41 RPM
SRP030211_testis	0.19 RPM	283.37 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1173 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021767	2 retrocopies	retro_btau_1173 , retro_btau_1614,
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Mus musculus	ENSMUSG00000074781	6 retrocopies	retro_mmus_1031, retro_mmus_2656, retro_mmus_3031, retro_mmus_3294, retro_mmus_3510, retro_mmus_524,
Nomascus leucogenys	ENSNLEG00000005695	2 retrocopies	retro_nleu_1078, retro_nleu_2279,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112, retro_ptro_3253, retro_ptro_956,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Sus scrofa	ENSSSCG00000000908	4 retrocopies	retro_sscr_101, retro_sscr_369, retro_sscr_698, retro_sscr_699,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,