RetrogeneDB ID: retro_cfam_587

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:5358883..5359723(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001397
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHB
• Ensembl ID: ENSCAFG00000015832
• Aliases: None
• Description: Canis lupus familiaris succinate dehydrogenase complex, subunit B, iron sulfur (Ip) (SDHB), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001252217]

Sequence

>retro_cfam_587
ATGGCGGCGGTGGTCGGAGTCTCCTTGAAACGCCGGTTCCCGGCTGCAGCCCTCGGCGGAGCCTGCCTGCAGGCCTGCCG
GGGGGAACAGACAGCGGCAGCCACAGCTCCCCGAATCAAGAAATTTGCCATCTACCGATGGGACCCAGACAAGACTGGAG
ATAAACCGCATATGCAGACTTATGAAATTGATTTGAATAAATGTGGTCCTATGGTGTTGGATGCTTTAATCAAGATTAAG
AATGAAATTGACTCTACCTTGACCTTCCGAAGATCATGCAGAGAAGGCATCTGTGGCTCCTGTGCCATGAACATCAACGG
AGGCAACACTCTGGCTTGCACCCGCCGGATCGACACCAACCTCAGCAAAGTCTCCAAAATCTACCCTCTGCCGCATATGT
ATGTGATAAAGGATCTGGTTCCTGACTTGAGCAACTTCTATGCTCAGTACAAATCCATTGAACCTTATTTGAAGAAGAAG
GATGAATCCCAGGAGGGCAAGCAGCAGTATCTGCAGTCCATAGAAGATCGTGAGAAACTGGACAGGCTGTACGAGTGTAT
CCTCTGTGCTTGCTGCAGCACCAGCTGCCCTAGCTACTGGTGGAATGGAGACAAATACCTGGGGCCTGCGGTTCTCATGC
AGGCCTACCGCTGGATGATCGACTCCAGAGACGACTTCACTGAGGAGCACCTGGCCAAGCTGCAGGACCCGTTCTCTCTG
TACCGCTGCCACACCATCATGAACTGCACAAGGACCTGCCCCAAGGGGCTGAATCCAGGCAAAGCTATTGCTGAAATCAA
GAAAATGATGGCCACCTATAAGGGGAAGAAAGCGTCCGTG

Alignment

ORF - retro_cfam_587 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAVVGVSLKRRFPAAALGGACLQACRGAQTAAATAPRIKKFAIYRWDPDKTGDKPHMQTYEIDLNKCGP
          MAAVVGVSLKRRFPAAALGGACLQACRG.QTAAATAPRIKKFAIYRWDPDKTGDKPHMQTYEIDLNKCGP
Retrocopy MAAVVGVSLKRRFPAAALGGACLQACRGEQTAAATAPRIKKFAIYRWDPDKTGDKPHMQTYEIDLNKCGP

Parental  MVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNINGGNTLACTRRIDTNLSKVSKIYPLPHMYVIKDLV
          MVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNINGGNTLACTRRIDTNLSKVSKIYPLPHMYVIKDLV
Retrocopy MVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNINGGNTLACTRRIDTNLSKVSKIYPLPHMYVIKDLV

Parental  PDLSNFYAQYKSIEPYLKKKDESQEGKQQYLQSIEDREKLDGLYECILCACCSTSCPSYWWNGDKYLGPA
          PDLSNFYAQYKSIEPYLKKKDESQEGKQQYLQSIEDREKLD.LYECILCACCSTSCPSYWWNGDKYLGPA
Retrocopy PDLSNFYAQYKSIEPYLKKKDESQEGKQQYLQSIEDREKLDRLYECILCACCSTSCPSYWWNGDKYLGPA

Parental  VLMQAYRWMIDSRDDFTEERLAKLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKGKKASV
          VLMQAYRWMIDSRDDFTEE.LAKLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKGKKASV
Retrocopy VLMQAYRWMIDSRDDFTEEHLAKLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKGKKASV

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	4.54 RPM	22.55 RPM
SRP017611_brain	10.96 RPM	14.21 RPM
SRP017611_kidney	59.17 RPM	89.35 RPM
SRP017611_liver	1.02 RPM	58.08 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_587 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DN331000	5358906	5359358	98.7	446	6	440

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_587 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015832	1 retrocopy	retro_cfam_587 ,
Choloepus hoffmanni	ENSCHOG00000005664	1 retrocopy	retro_chof_2016,
Callithrix jacchus	ENSCJAG00000007927	1 retrocopy	retro_cjac_2988,
Loxodonta africana	ENSLAFG00000018475	1 retrocopy	retro_lafr_454,
Macropus eugenii	ENSMEUG00000004817	1 retrocopy	retro_meug_1106,
Microcebus murinus	ENSMICG00000016629	1 retrocopy	retro_mmur_1062,
Myotis lucifugus	ENSMLUG00000000032	1 retrocopy	retro_mluc_150,
Nomascus leucogenys	ENSNLEG00000013264	1 retrocopy	retro_nleu_1640,
Sorex araneus	ENSSARG00000013780	1 retrocopy	retro_sara_577,
Tupaia belangeri	ENSTBEG00000004803	2 retrocopies	retro_tbel_2480, retro_tbel_2875,
Xenopus tropicalis	ENSXETG00000013435	1 retrocopy	retro_xtro_60,