RetrogeneDB ID: retro_cfam_1888

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:71145360..71146428(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSCAFG00000030749
• Aliases: None
• Description: farnesyl diphosphate synthase [Source:HGNC Symbol;Acc:3631]

Sequence

>retro_cfam_1888
CTGACATCCAGGAGCAGAATGAATGGAGCCCAGAAGTTGGACGCTTATGCCCAAGCAAGGCAGGATTTCATCCAGCACTT
CCCCCAGATTGTCAAGATGCTGACTGAGGATGGCATGGGCCACCTAGAGATGGGAGATGCTATTGCCCAGCTCAAGGAAG
TCTTGGAGTACAATGCTGTTGGAGGCAAGTACCAGCAGGTTTTGACTGTGTTGATAGCATTTCAGGAGCTGGTGGATCCC
AGGAAGCAGGATGCTGCTAGTCTGCAGTGAGCCCTGACTGTGGGCTGGTGTATGGAGCTGCTCCAGGCTTTCTTCCTGGT
GTCAGATGATATCATGGACTCGTCTCTCACCCAACAGGGGCAGATCTGTTGGTATCAGAAGCCAGGCATAGGCTTGGATG
CCATCAATGATGCTTTGCTTCTGGAAGCATGTATCTACTGCCTGCTGAAGGTCTACTGCCAGGAGCAGCCCTATTACCTG
GACCTGATTGAGCTTTTCCTCCAGAGTTCCTACCAGACTGAGATTGGACAGACCCTGGACCTCATCACCTCCCCACAGGG
CAGCGTGGATCTCAGCAGGTTCACTGAGAAGAGGTACAAGTCTATTGTCAAGTGCAAGATGGCCTTCTACTCGTTATATC
TTCCCATGGCTGCTGCCATGTATATGTAAGGGATCGATGGGGAGAAAGAGCATGCCAATGCTAAGAAGATCCTGCTGAAT
ATGGGGGAGTTCTTTCAGATTCAGGATGATTTCCTGGATCTCTTTGGGGATCCCAGTGTGACAGGTAAGATTGGCACAGA
TATTCAGGACAACAAGTGCAGCTGGTTGGTGGTTCAGTGTCTGCAGCAGGCATCTCCAGAGGAGTGGAAGGAGAATTATG
GGCAGAAAGAGCCAGAGAAGGTGGCCCGGGTGAAGGTGCTGTAGGAGGAGCTGAACCTGCTGGCCAATTTCACCCAGTAT
GAGGAAGACAGCTACAGCCATCTCATGAGCCTCATCGAGCAGTGCGCCTTGCCCTTGCCCCCAGCCATCTTCTTGGGCCT
TGTGCACAATATCTACAAGAGGAAAAAG

Alignment

ORF - retro_cfam_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.86 %
• Parental protein coverage: 85.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYSSLRMNGDQKLDAYAQARQDFIQHFPQIVKILTEDGMGHPETGDAIARLKEVLEYNAVGGKYQRGLTV
          L.S..RMNG.QKLDAYAQARQDFIQHFPQIVK.LTEDGMGH.E.GDAIA.LKEVLEYNAVGGKYQ..LTV
Retrocopy LTSRSRMNGAQKLDAYAQARQDFIQHFPQIVKMLTEDGMGHLEMGDAIAQLKEVLEYNAVGGKYQQVLTV

Parental  LIAFQELVEPRKQDAASLRRALTVGWCVELLQAFFLVSDDIMDSSLTRRGQICWYQKPGIGLDAINDALL
          LIAFQELV.PRKQDAASL..ALTVGWC.ELLQAFFLVSDDIMDSSLT..GQICWYQKPGIGLDAINDALL
Retrocopy LIAFQELVDPRKQDAASLQ*ALTVGWCMELLQAFFLVSDDIMDSSLTQQGQICWYQKPGIGLDAINDALL

Parental  LEACIYRLLKVYCREQPYYLNLIELFLQSSYQTEIGQTLDLITAPQGSVDLSRFTEKRYKSIVKYKTAFY
          LEACIY.LLKVYC.EQPYYL.LIELFLQSSYQTEIGQTLDLIT.PQGSVDLSRFTEKRYKSIVK.K.AFY
Retrocopy LEACIYCLLKVYCQEQPYYLDLIELFLQSSYQTEIGQTLDLITSPQGSVDLSRFTEKRYKSIVKCKMAFY

Parental  SFYLPVAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDFLDLFGDPSVTGKIGTDIQDNKCSWLVVQC
          S.YLP.AAAMYM.GIDGEKEHANAKKILL.MGEFFQIQDDFLDLFGDPSVTGKIGTDIQDNKCSWLVVQC
Retrocopy SLYLPMAAAMYM*GIDGEKEHANAKKILLNMGEFFQIQDDFLDLFGDPSVTGKIGTDIQDNKCSWLVVQC

Parental  LQQASPEQRKVLQENYGQKEAEKVARVKALYEELNLPAVFTQYEEDSYSRLMSLIERCASPLPPAIFLGL
          LQQASPE..K...ENYGQKE.EKVARVK.L.EELNL.A.FTQYEEDSYS.LMSLIE.CA.PLPPAIFLGL
Retrocopy LQQASPEEWK---ENYGQKEPEKVARVKVL*EELNLLANFTQYEEDSYSHLMSLIEQCALPLPPAIFLGL

Parental  AHNIYKRKK
          .HNIYKRKK
Retrocopy VHNIYKRKK

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	76.27 RPM
SRP017611_brain	0.00 RPM	58.12 RPM
SRP017611_kidney	0.00 RPM	49.92 RPM
SRP017611_liver	0.00 RPM	62.87 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1888 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1888 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030749	2 retrocopies	retro_cfam_1822, retro_cfam_1888 ,
Callithrix jacchus	ENSCJAG00000008364	11 retrocopies	retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011, retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi	ENSETEG00000001154	6 retrocopies	retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Macaca mulatta	ENSMMUG00000023144	3 retrocopies	retro_mmul_1190, retro_mmul_2152, retro_mmul_565,
Mus musculus	ENSMUSG00000059743	5 retrocopies	retro_mmus_1028, retro_mmus_1552, retro_mmus_2802, retro_mmus_3625, retro_mmus_590,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Rattus norvegicus	ENSRNOG00000043377	3 retrocopies	retro_rnor_1175, retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus	ENSSTOG00000004475	1 retrocopy	retro_itri_488,
Tursiops truncatus	ENSTTRG00000013326	1 retrocopy	retro_ttru_689,