RetrogeneDB ID: retro_cfam_78

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:23277232..23277562(+)
• Located in intron of: ENSCAFG00000014252

Retrocopy information

• Ensembl ID: ENSCAFG00000023760
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTMA
• Ensembl ID: ENSCAFG00000032596
• Aliases: None
• Description: Canis lupus familiaris prothymosin, alpha (PTMA), mRNA. [Source:RefSeq mRNA;Acc:NM_001252198]

Sequence

>retro_cfam_78
ATGTCAGAAGCGTCTGTGGACACCAGCTCCGAGATCACCACCAAGGACTTAAAGGAGAAGAAGGAAGTTGTGGAGGAGGC
AGAGAATGGAAGAGACGCGCCTGCTAATGGGAACGCTAATGAGGAAAATGGGGAGCAGGAGGCTGACAATGAGGTAGAGG
AAGGAGGGGAGGAAGAGGAGGAGGAGGAGGAGGAGGAGGAAGGCGATGGAGAGGAAGAGGATGGAGATGAAGATGAGGAG
GCCGAGGCAGGTACGGGCAAACGGGCAGCTGAAGACGATGAGAATGACAACATCAACCCCAAGAAGCAGAAGACTGATGA
GGATGACTAG

Alignment

ORF - retro_cfam_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDAAVDTSSEITTKDLKEKKEVVEEAENGRDAPANGNAENEENGEQEADNEVDEEEEEGGEEEEEEEEG
          MS.A.VDTSSEITTKDLKEKKEVVEEAENGRDAPANGNA.NEENGEQEADNEV.E..EE..EEEEEEEEG
Retrocopy MSEASVDTSSEITTKDLKEKKEVVEEAENGRDAPANGNA-NEENGEQEADNEVEEGGEE-EEEEEEEEEG

Parental  DGEEEDGDEDEEAEAATGKRAAEDDEDDDVDTKKQKTDEDD
          DGEEEDGDEDEEAEA.TGKRAAEDDE.D....KKQKTDEDD
Retrocopy DGEEEDGDEDEEAEAGTGKRAAEDDENDNINPKKQKTDEDD

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
SRP012049_cerebellum	22.64 RPM	592.31 RPM
SRP017611_brain	9.84 RPM	212.06 RPM
SRP017611_kidney	13.08 RPM	278.28 RPM
SRP017611_liver	8.48 RPM	163.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_78 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
GR886284	23277258	23277390	99.3	131	1	130

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_78 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_78 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,