RetrogeneDB ID: retro_cfam_1425

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:39541700..39541937(-)
• Located in intron of: ENSCAFG00000018100

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR3
• Ensembl ID: ENSCAFG00000029975
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 [Source:HGNC Symbol;Acc:15606]

Sequence

>retro_cfam_1425
AGACGCGGTTTCTTACCTTCTTTTGCCCCTGCAACAGACCAAGGGGGCAAACTTGGACTCTCAAAAAATAAAAATATCAC
CTGTTACTGTAACACCTATCAGGTGTTTCAATTCAATGATTTACTTTTGGTACCGAGTTTCCTGGCCTGCAGCAATGGCA
ATAAGGGACTCATTGTCAGCCTAGAAAAGGAACTTGTTCTGTTATTTGAAGAACTGAGACAAATTGTGGAAGTTTCT

Alignment

ORF - retro_cfam_1425 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 63.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSNANTGLIVSLEKELAPLFE
          R.GFL..FA.ATDQG.KLGLSKNK.I.CY.NTYQV.QFN.L.LV.SF.A.SN.N.GLIVSLEKEL..LFE
Retrocopy RRGFLPSFAPATDQGGKLGLSKNKNITCYCNTYQVFQFNDLLLVPSFLACSNGNKGLIVSLEKELVLLFE

Parental  ELRQVVEVS
          ELRQ.VEVS
Retrocopy ELRQIVEVS

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	0.00 RPM	20.54 RPM
SRP017611_brain	0.00 RPM	20.88 RPM
SRP017611_kidney	0.00 RPM	41.34 RPM
SRP017611_liver	0.00 RPM	7.32 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1425 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1425 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007923	1 retrocopy	retro_btau_578,
Canis familiaris	ENSCAFG00000029975	3 retrocopies	retro_cfam_1425 , retro_cfam_692, retro_cfam_700,
Choloepus hoffmanni	ENSCHOG00000013153	7 retrocopies	retro_chof_1167, retro_chof_1236, retro_chof_1266, retro_chof_1536, retro_chof_166, retro_chof_1929, retro_chof_955,
Callithrix jacchus	ENSCJAG00000015196	4 retrocopies	retro_cjac_1149, retro_cjac_1821, retro_cjac_2581, retro_cjac_2786,
Cavia porcellus	ENSCPOG00000013304	2 retrocopies	retro_cpor_112, retro_cpor_208,
Echinops telfairi	ENSETEG00000009065	6 retrocopies	retro_etel_1271, retro_etel_1421, retro_etel_1621, retro_etel_1639, retro_etel_471, retro_etel_794,
Homo sapiens	ENSG00000109270	2 retrocopies	retro_hsap_1190, retro_hsap_3374,
Gorilla gorilla	ENSGGOG00000001132	2 retrocopies	retro_ggor_2283, retro_ggor_928,
Monodelphis domestica	ENSMODG00000020688	3 retrocopies	retro_mdom_1133, retro_mdom_455, retro_mdom_907,
Mustela putorius furo	ENSMPUG00000009569	2 retrocopies	retro_mputfur_590, retro_mputfur_877,
Mus musculus	ENSMUSG00000091512	1 retrocopy	retro_mmus_167,
Nomascus leucogenys	ENSNLEG00000013684	2 retrocopies	retro_nleu_1936, retro_nleu_965,
Otolemur garnettii	ENSOGAG00000005336	4 retrocopies	retro_ogar_2081, retro_ogar_2120, retro_ogar_3435, retro_ogar_451,
Pongo abelii	ENSPPYG00000014955	3 retrocopies	retro_pabe_1268, retro_pabe_2772, retro_pabe_991,
Pan troglodytes	ENSPTRG00000016310	1 retrocopy	retro_ptro_2294,
Pteropus vampyrus	ENSPVAG00000017674	1 retrocopy	retro_pvam_1378,
Rattus norvegicus	ENSRNOG00000010552	1 retrocopy	retro_rnor_2341,
Sus scrofa	ENSSSCG00000009176	1 retrocopy	retro_sscr_148,
Tupaia belangeri	ENSTBEG00000003682	6 retrocopies	retro_tbel_1932, retro_tbel_2172, retro_tbel_230, retro_tbel_3358, retro_tbel_4521, retro_tbel_924,
Tursiops truncatus	ENSTTRG00000015015	1 retrocopy	retro_ttru_809,