RetrogeneDB ID: retro_cfam_2043

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:10616520..10617150(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011827
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSTP1
• Ensembl ID: ENSCAFG00000011349
• Aliases: None
• Description: Canis lupus familiaris glutathione S-transferase pi 1 (GSTP1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252167]

Sequence

>retro_cfam_2043
ATGCCACCCTACACCATCACCTACTTCCCTGTTCGAGGGCGCTGTGAGGCCATGCGCATGCTGCTGGCTGACCAGGGCCA
GAGCTGGAAGGAGGAGGTGGTGACCATGGAGACCTGGATGAAGGGCTCACTCAAGGCCTCCTGTCTGTACGGGCAGCTCC
CCAAGTTCCAGGACGGAGACCTCACCCTGTACCAGTCCAATGCCATCCTGCGACACCTGGGCCGCTCCCTTGGGCTCTAC
GGGAAGGACCAGCAGGAGGCGGCCTTGCTGGATGTAGTGAACGATGGTGTGGAGGATCTCCGCTGCAAATACGCCCTCCT
CATCTACACTAACTATGAGGCAGGAAAGGAGGAGTATGTGAAGGCACTACCAGGTTACCTGAAGCCTTTTGAAACGCTGT
TGTCCCAGAATGAGGGGGGCCAGGCCTTCATCGTGGGCAACCAGATCTCCTTCGCGGACTACAACCTGCTGGACTTGCTG
CTGATTCACCAGGTCCTGGCCCCCAGCTGCCTGGACTCCTTCCCCCTGCTCTCGGCCTATGTGGCGCGCCTCAGCGCCAG
ACCCAAGCTCAAGGCATTCCTGTCGTCCCCCGAGCACGTGAACCGCCCCATCAATGGCAACGGGAAGCAG

Alignment

ORF - retro_cfam_2043 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPYTITYFPVRGRCEAMRMLLADQGQSWKEEVVTMETWMKGSLKASCLYGQLPKFQDGDLTLYQSNAIL
          MPPYTITYFPVRGRCEAMRMLLADQGQSWKEEVVTMETWMKGSLKASCLYGQLPKFQDGDLTLYQSNAIL
Retrocopy MPPYTITYFPVRGRCEAMRMLLADQGQSWKEEVVTMETWMKGSLKASCLYGQLPKFQDGDLTLYQSNAIL

Parental  RHLGRSLGLYGKDQQEAALLDVVNDGVEDLRCKYALLIYTNYEAGKEEYVKALPGYLKPFETLLSQNEGG
          RHLGRSLGLYGKDQQEAALLDVVNDGVEDLRCKYALLIYTNYEAGKEEYVKALPGYLKPFETLLSQNEGG
Retrocopy RHLGRSLGLYGKDQQEAALLDVVNDGVEDLRCKYALLIYTNYEAGKEEYVKALPGYLKPFETLLSQNEGG

Parental  QAFIVGNQISFADYNLLDLLLIHQVLAPSCLDSFPLLSAYVARLSARPKLKAFLSSPEHVNRPINGNGKQ
          QAFIVGNQISFADYNLLDLLLIHQVLAPSCLDSFPLLSAYVARLSARPKLKAFLSSPEHVNRPINGNGKQ
Retrocopy QAFIVGNQISFADYNLLDLLLIHQVLAPSCLDSFPLLSAYVARLSARPKLKAFLSSPEHVNRPINGNGKQ

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	2.77 RPM	88.32 RPM
SRP017611_brain	0.40 RPM	43.51 RPM
SRP017611_kidney	0.53 RPM	292.35 RPM
SRP017611_liver	0.65 RPM	144.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2043 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2043 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043 , retro_cfam_46, retro_cfam_617,
Canis familiaris	ENSCAFG00000019812	2 retrocopies	retro_cfam_1766, retro_cfam_2062,
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Macropus eugenii	ENSMEUG00000001519	2 retrocopies	retro_meug_1519, retro_meug_1762,
Myotis lucifugus	ENSMLUG00000011529	4 retrocopies	retro_mluc_1669, retro_mluc_1714, retro_mluc_1962, retro_mluc_629,
Mustela putorius furo	ENSMPUG00000004029	2 retrocopies	retro_mputfur_1215, retro_mputfur_1463,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Oryctolagus cuniculus	ENSOCUG00000002230	1 retrocopy	retro_ocun_391,
Pteropus vampyrus	ENSPVAG00000008586	6 retrocopies	retro_pvam_1119, retro_pvam_1463, retro_pvam_568, retro_pvam_664, retro_pvam_681, retro_pvam_718,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842, retro_rnor_769,
Tursiops truncatus	ENSTTRG00000003746	1 retrocopy	retro_ttru_1416,
Vicugna pacos	ENSVPAG00000008003	1 retrocopy	retro_vpac_73,