RetrogeneDB ID: retro_cfam_94

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:30713795..30714341(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000005346
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSCAFG00000018545
• Aliases: None
• Description: malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]

Sequence

>retro_cfam_94
ATGTTCAAGAAATTCGACGAGAAGGAAAACGTGTCCAACTGCATCCAGCTGAAGACGTCCGTCATCAAGGGCATTAAGAA
CCAGCTGATAGAGCAGTTCCCGGGCATCGAGCCGTGGCTCAACCAGATCCTGCCCAAGAAGGACCCGGTGAAGATCGTGC
GCTGCCACGAGCACATAGAGATCCTCACGGTGAACGGCGAGCTCCTGTTCTTCAGGCAGAGGGAGGGGCCCTTCTACCCG
ACGCTGCGGCTGCTGCACAAGTACCCGTTCATCCTGCCGCACCAGCAGGTGGACAAGGGCGCCATCAAGTTCGTGCTCAG
CGGGGCCAACATCATGTGCCCCGGCCTGACCTCGCCCGGCGCGCAGCTCTACCCCGCCGCCGTCGACACGGTCGTGGCCA
TCATGGCGGAGGGCAAGCAGCACGCGCTGTGCGTCGGGGTCATGCGCATGTCGGCGGAGGACATCGAGAAGGTCAACAAG
GGCATCGGCATCGAGAACATCCACTACCTCAACGACGGGCTGTGGCACATGAAGACGTACAAGTGA

Alignment

ORF - retro_cfam_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
          MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQI.PKKDPVKIVRCHEHIEILTVNGELLF
Retrocopy MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQILPKKDPVKIVRCHEHIEILTVNGELLF

Parental  FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQ
          FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGA.LYPAAVDT.VAIMAEGKQ
Retrocopy FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAQLYPAAVDTVVAIMAEGKQ

Parental  HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          HALCVGVM.MSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
Retrocopy HALCVGVMRMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK

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	22.51 RPM	5.92 RPM
SRP017611_brain	21.28 RPM	5.16 RPM
SRP017611_kidney	32.82 RPM	27.67 RPM
SRP017611_liver	15.08 RPM	8.34 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_94 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_94 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_94 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_116

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94 ,
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Felis catus	ENSFCAG00000008448	2 retrocopies	retro_fcat_1009, retro_fcat_310,
Macropus eugenii	ENSMEUG00000014328	1 retrocopy	retro_meug_1518,
Macaca mulatta	ENSMMUG00000009043	1 retrocopy	retro_mmul_626,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Nomascus leucogenys	ENSNLEG00000015021	1 retrocopy	retro_nleu_2442,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pongo abelii	ENSPPYG00000020687	2 retrocopies	retro_pabe_1786, retro_pabe_1833,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Vicugna pacos	ENSVPAG00000001801	1 retrocopy	retro_vpac_138,