RetrogeneDB ID: retro_cfam_1780

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:9786705..9787191(+)
• Located in intron of: ENSCAFG00000014942

Retrocopy information

• Ensembl ID: ENSCAFG00000014950
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNAP23
• Ensembl ID: ENSCAFG00000011105
• Aliases: None
• Description: synaptosomal-associated protein, 23kDa [Source:HGNC Symbol;Acc:11131]

Sequence

>retro_cfam_1780
GAGCAACTAAACCGCATAGAAGAAGGCATGGACCAAATAAATAAAGACATGAGAGAGGCAGAGAAGACTTTAACGGAACT
CAACAAGTGCTGTGGCCTTTGTGTCTGTCCATGTAATAGGACAAAGAACTTTGAGTCCAGTAAGGCCTACAAGGCAACAT
GGGGAGATGGTGAAGACAACTCTCCTAGCAATGTAGTATCTAAGCAGCCAGGCCGAGTGACAAATGGGCAGCCTCAACAA
CCAGCCACTGGAGCAGTTAGCGGTGGATACATTAAACGTATAACTAATGATGCTAGAGAAGATGAGATGGAAGAGAACCT
GACTCAAGTGGGCAGTATCCTAGGAAACCTAAAAAACATGGCCCTGGAAATGGGCAATGAGATCGAGGCTCAAAATCGAA
AAATAGACCGGATCACAGAAAAGGCTGACACCAACAACGATCGTATTGATATTGCCAATGCCAGAGCAAAGAAACTCATT
GACAGC

Alignment

ORF - retro_cfam_1780 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 76.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQLNRIEEGMDQINKDMREAEKTLTELNKCCGLCVCPCNRTKNFESSKAYKATWGDGEDNSPSNVVSKQP
          EQLNRIEEGMDQINKDMREAEKTLTELNKCCGLCVCPCNRTKNFESSKAYKATWGDGEDNSPSNVVSKQP
Retrocopy EQLNRIEEGMDQINKDMREAEKTLTELNKCCGLCVCPCNRTKNFESSKAYKATWGDGEDNSPSNVVSKQP

Parental  GRVTNGQPQQPATGAVSGGYIKRITNDAREDEMEENLTQVGSILGNLKNMALEMGNEIEAQNRKIDRITE
          GRVTNGQPQQPATGAVSGGYIKRITNDAREDEMEENLTQVGSILGNLKNMALEMGNEIEAQNRKIDRITE
Retrocopy GRVTNGQPQQPATGAVSGGYIKRITNDAREDEMEENLTQVGSILGNLKNMALEMGNEIEAQNRKIDRITE

Parental  KADTNKDRIDIANARAKKLIDS
          KADTN.DRIDIANARAKKLIDS
Retrocopy KADTNNDRIDIANARAKKLIDS

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	4.83 RPM
SRP017611_brain	0.16 RPM	6.11 RPM
SRP017611_kidney	0.46 RPM	18.75 RPM
SRP017611_liver	0.36 RPM	3.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1780 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780 ,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,