RetrogeneDB ID: retro_cfam_1962

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:44082859..44083346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR1
• Ensembl ID: ENSCAFG00000005788
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 [Source:HGNC Symbol;Acc:26068]

Sequence

>retro_cfam_1962
ATGGAGTGCTGCTACAAGCAGCAAGAATGAAGACTTGGACCAGGCCCAGGACCAAGACGAGCAGAAGCTACTGCTGGACC
CTAGAAGCTCCTCTGCCAAAGCCCTCAAAGGAGTTGACTACCACAGCCTACTTTCCACTCACACAGATGAGCAGGGCCTG
CTCTCCTCCTCCTTGCTAAGATAGCCCCCAACATCGTTGACACATCTGCTGTGGACTCCCAGAGCATGGAGCAGCATGAG
TACATGGACTAAGCAAGGAAGGCAGCACAGCACCCACTTGGCTATGCTGAGCAGCAGTCTGCCCCACCAGAAGAAGCTGC
TGCCGCCACAATCTCTCACCAGCCAGCCCCACCAAATGGTGGCCAGCAAGCCCATCCCCTTCTCCGACTTGCAGCAGGTC
TCCAAGATAGCTGTTTATGCCTACAATGCACTTTCTCAGATCCAAGTGGATGCAAAAAAGGAGCTGGTTGTACAGTTTGG
GGCTCCT

Alignment

ORF - retro_cfam_1962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGCCY-SSENEDSDQ--DREERKLLLDPSSPPTKALNGAEPNYHSLPPTRTDEQALLS-SILAKTASNII
          M.CCY.SS.NED.DQ..D..E.KLLLDP.S...KAL.G....YHSL..T.TDEQ.LLS.S.L........
Retrocopy MECCY>SSKNEDLDQAQDQDEQKLLLDPRSSSAKALKGVD--YHSLLSTHTDEQGLLSSSLLR*PPTSLT

Parental  DVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIA
          ...................RQ.ST.LA.LSSSL.H.KKL.P..SLTSQPHQ..AS.PIPFSDLQQVS.IA
Retrocopy HLLWTPRAWSSMSTWTKQGRQHSTHLAMLSSSLPHQKKLLPPQSLTSQPHQMVASKPIPFSDLQQVSKIA

Parental  AYAYSALSQIRVDAKEELVVQFGIP
          .YAY.ALSQI.VDAK.ELVVQFG.P
Retrocopy VYAYNALSQIQVDAKKELVVQFGAP

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	0.04 RPM	24.57 RPM
SRP017611_brain	0.16 RPM	20.32 RPM
SRP017611_kidney	0.26 RPM	37.84 RPM
SRP017611_liver	0.00 RPM	12.62 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1962 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010854	2 retrocopies	retro_amel_1176, retro_amel_436,
Canis familiaris	ENSCAFG00000005788	1 retrocopy	retro_cfam_1962 ,
Echinops telfairi	ENSETEG00000010979	1 retrocopy	retro_etel_1005,
Felis catus	ENSFCAG00000005320	2 retrocopies	retro_fcat_142, retro_fcat_496,
Macropus eugenii	ENSMEUG00000003560	1 retrocopy	retro_meug_17,
Myotis lucifugus	ENSMLUG00000014117	1 retrocopy	retro_mluc_2372,
Mustela putorius furo	ENSMPUG00000010289	3 retrocopies	retro_mputfur_1178, retro_mputfur_270, retro_mputfur_455,
Tarsius syrichta	ENSTSYG00000014730	2 retrocopies	retro_tsyr_1324, retro_tsyr_33,