RetrogeneDB ID: retro_btau_143

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:47998758..47999088(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000016081
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTMA
• Ensembl ID: ENSBTAG00000002549
• Aliases: None
• Description: Prothymosin alpha Thymosin alpha-1 [Source:UniProtKB/Swiss-Prot;Acc:P01252]

Sequence

>retro_btau_143
ATGTCAGACGCGGCCGTGGACAACAGCTCCGAGATCACCACCAAGGACTTAAAGGAGAAGAAGGAAGTTGTGGAGGAGGC
GGAGAATGGGAGAGAGGCACCTGCAAATGGGAATGCTAATGAGGAAAATGGGGAGCAGGAAGCAGACAACGAGGTAGACG
AAGAAGAGGAGGAAGGTGGGGAGGAAGAGGAGGAGGAGGAAGGTGACGGTGAGGAAGAGGACGGAGATGAAGATGAGGAG
GCCGAGGCAGCTACGGGCAAACGGGCAGCTGAAGATGACGAGGATAACGATGTGGATACCAAGAAGCAGAAGACTGATAA
AGATGACTAG

Alignment

ORF - retro_btau_143 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDAAVDTSSEITTKDLKEKKEVVEEAENGREAPANGNANEENGEQEADNEVDEEEEEGGEEEEEEEEGD
          MSDAAVD.SSEITTKDLKEKKEVVEEAENGREAPANGNANEENGEQEADNEVDEEEEEGGEEEEEEE.GD
Retrocopy MSDAAVDNSSEITTKDLKEKKEVVEEAENGREAPANGNANEENGEQEADNEVDEEEEEGGEEEEEEE-GD

Parental  GEEEDGDEDEEAEAATGKRAAEDDEDDDVDTKKQKTDEDD
          GEEEDGDEDEEAEAATGKRAAEDDED.DVDTKKQKTD.DD
Retrocopy GEEEDGDEDEEAEAATGKRAAEDDEDNDVDTKKQKTDKDD

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	0.22 RPM	263.15 RPM
ERP005899_muscle	4.54 RPM	575.93 RPM
SRP017611_brain	1.55 RPM	92.77 RPM
SRP017611_kidney	1.72 RPM	205.44 RPM
SRP017611_liver	1.13 RPM	118.70 RPM
SRP030211_testis	0.70 RPM	144.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_143 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_143 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002549	2 retrocopies	retro_btau_1034, retro_btau_143 ,
Canis familiaris	ENSCAFG00000032596	4 retrocopies	retro_cfam_113, retro_cfam_1570, retro_cfam_282, retro_cfam_78,
Callithrix jacchus	ENSCJAG00000013611	9 retrocopies	retro_cjac_1484, retro_cjac_1976, retro_cjac_2318, retro_cjac_2507, retro_cjac_2611, retro_cjac_3035, retro_cjac_3151, retro_cjac_421, retro_cjac_647,
Felis catus	ENSFCAG00000004780	1 retrocopy	retro_fcat_1682,
Homo sapiens	ENSG00000187514	6 retrocopies	retro_hsap_1863, retro_hsap_2690, retro_hsap_3447, retro_hsap_4198, retro_hsap_4288, retro_hsap_4787,
Gorilla gorilla	ENSGGOG00000009874	4 retrocopies	retro_ggor_1551, retro_ggor_2149, retro_ggor_2981, retro_ggor_952,
Myotis lucifugus	ENSMLUG00000002628	2 retrocopies	retro_mluc_131, retro_mluc_26,
Macaca mulatta	ENSMMUG00000012140	1 retrocopy	retro_mmul_196,
Mus musculus	ENSMUSG00000026238	4 retrocopies	retro_mmus_3135, retro_mmus_3136, retro_mmus_414, retro_mmus_55,
Nomascus leucogenys	ENSNLEG00000014135	2 retrocopies	retro_nleu_30, retro_nleu_96,
Rattus norvegicus	ENSRNOG00000018584	1 retrocopy	retro_rnor_69,
Sus scrofa	ENSSSCG00000023690	1 retrocopy	retro_sscr_895,