RetrogeneDB ID: retro_cfam_1438

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 31:22125294..22126035(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GGPS1
• Ensembl ID: ENSCAFG00000011303
• Aliases: None
• Description: geranylgeranyl diphosphate synthase 1 [Source:HGNC Symbol;Acc:4249]

Sequence

>retro_cfam_1438
ATGGAGATGACTCAAGAAACAGTCCAAAGAGTTCTTCTAGAACCCTATAAATATTTACTTCAGTTATCAGGTAAACAAGT
GAGGACCAAACTTTCACAGGCATTTAATCATTGGCTAAAAGTTCCAGAAGATAAGCCACAGATTATCATTGAAGGGACAG
AAATGTTGCATAATGCCAGTTTGCTCATCGATGATAGTGAAGACAACTCAAAACTTCGACGTGGCTTTCCAGTGGCACAC
AGCATCTATGGAATTCCATCTGTCATCAATTCTGCCAATTATGTATATCTTCTTGGCCTACAGAAAGTCTTAACCCTTGA
CCACCCAGATGCAGTGAAGCTTTTTACCCTCCAGCTTTTGGAACTCCATCAGGGACAAGGTCTAGACATTTATTGGAGGG
ATAATTACACTTGTCCCTCTGAAGAAGAATATAAAGCTATGGTGCTGCAAAAGACAGGTGGACTATTTGGATTAGCAGTA
GGTCTCATGCAGTTGTTCTCTGATTACAAAGAAGATCTGAAGCCACTACTTAATACACTTGGGCTCTTTTTCCAAATTAG
GGATGATTATGCTAATCTACACTCCAAAGAATACAGTGAAAACAAAAGCTTTTGTGAAGATCTAACAGAGGGAAAGTTCT
CATTCCCTACTATTCAGGCTATTTGGTCGAGGCCTGAAAGCACCCAGGTGCAGAATATCTTGCGCCAGAGAACCGAAAAT
ATAGATATTAAAAAAAAATGC

Alignment

ORF - retro_cfam_1438 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 82.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKTQETVQRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNS
          ME.TQETVQR.LLEPYKYLLQL.GKQVRTKLSQAFNHWLKVPEDK.QIIIE.TEMLHNASLLIDD.EDNS
Retrocopy MEMTQETVQRVLLEPYKYLLQLSGKQVRTKLSQAFNHWLKVPEDKPQIIIEGTEMLHNASLLIDDSEDNS

Parental  KLRRGFPVAHSIYGIPSVINSANYVYFLGLQKVLTLDHPDAVKLFTHQLLELHQGQGLDIYWRDNYTCPT
          KLRRGFPVAHSIYGIPSVINSANYVY.LGLQKVLTLDHPDAVKLFT.QLLELHQGQGLDIYWRDNYTCP.
Retrocopy KLRRGFPVAHSIYGIPSVINSANYVYLLGLQKVLTLDHPDAVKLFTLQLLELHQGQGLDIYWRDNYTCPS

Parental  EEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTE
          EEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTE
Retrocopy EEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTE

Parental  GKFSFPTIHAIWSRPESTQVQNILRQRTENIDIKKYC
          GKFSFPTI.AIWSRPESTQVQNILRQRTENIDI...C
Retrocopy GKFSFPTIQAIWSRPESTQVQNILRQRTENIDIXXXC

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	6.93 RPM
SRP017611_brain	0.00 RPM	7.07 RPM
SRP017611_kidney	0.00 RPM	13.93 RPM
SRP017611_liver	0.07 RPM	3.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1438 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1438 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011303	1 retrocopy	retro_cfam_1438 ,
Echinops telfairi	ENSETEG00000008916	1 retrocopy	retro_etel_1265,
Myotis lucifugus	ENSMLUG00000016813	1 retrocopy	retro_mluc_54,
Mus musculus	ENSMUSG00000021302	1 retrocopy	retro_mmus_1253,
Ictidomys tridecemlineatus	ENSSTOG00000004263	1 retrocopy	retro_itri_619,