RetrogeneDB ID: retro_cfam_2104

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:80875245..80876228(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000017969
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RABGGTB
• Ensembl ID: ENSCAFG00000020392
• Aliases: None
• Description: Rab geranylgeranyltransferase, beta subunit [Source:HGNC Symbol;Acc:9796]

Sequence

>retro_cfam_2104
GGCACACTGCAGAAGGATGTTATCATCAAGTCAGGTGCACCTGACACGCTGCTGTTAGAGAAGCATGTGGATTATATCGC
ATCCTATGGCTCCAAGAAAGATGATTATGAATACTGTATGCCTGAATATTTGAGAATGAGTGGGATCTATTGGGGTCTGA
CTGTAATGGATCTGATGGGACAACTACATCGGATGAATAGAGAAGAAATTCTGACCTTCATTAAGTCATGTCAACATGAG
TGTGGTGGAATAAGTGCTAGTATTGGACATGACCCCCATCTTTTGTACACTCTAAGTGCTGTCCAGATTCTTACTCTGTA
TGATAGTATTGTTATTGATGTAAATAAAGTTGTGGAATATGTTCAGAGTCTACAGAAAGAAGATGGTTCTTTTGCTGGAG
ATATATGGGGAGAAATAGATACAAGATTCTCTTTTAGTGCGGTGGCAACCTTGGCTCTGTTGGGGAAGCTAGACACTATT
AATGTGGGAAAGGCAATTGAATTTGTTTTATCGTGTATGAACTTTGTTGGTGGATTTGGTTGCAGGCCAGGTTCTGAATC
CCATGCTGGGCAGATCTATTGTTGCACAGGATTTCTGGCTATTACTAGCCAGTTGCATCAAGTAAATTCTGATTTACTCG
GTTGGTGGCTTTGTGAACAACAGTTACCATCAGGTGGACTCAATGGAAGGCCCGAGAAGTTACCAGATGTCTGCTATTCG
TGGTGGGTGTTGGCTTCCCTAAAGATAATTGGAAGGCTTCATTGGATTGATAGAAACTGCGAAGTTTCATTTTAGCATGT
CAAGATGAAGAAACAGGAGGATTTGTAGACCGACCGGGAGACATGGTAGATCCTTTTCATACTTTATTTGGAATTGCTGG
ATTGTCACTTCTGGGAGAAGAACAGATTAAACCTGTTAGTCCTGTTTTTTGCATGCCTGAATAAGTGCTTCGGAGAGTCA
ATGTTCAGCCTAAACTAGTGAGC

Alignment

ORF - retro_cfam_2104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.84 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTPQKDVIIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLTVMDLMGQLHRMNREEI
          GT.QKDVIIKS.APDTLLLEKH.DYIASYGSKKDDYEYCM.EYLRMSGIYWGLTVMDLMGQLHRMNREEI
Retrocopy GTLQKDVIIKSGAPDTLLLEKHVDYIASYGSKKDDYEYCMPEYLRMSGIYWGLTVMDLMGQLHRMNREEI

Parental  LTFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVIDVNKVVEYVQSLQKEDGSFAGDIWGEI
          LTFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSI.VIDVNKVVEYVQSLQKEDGSFAGDIWGEI
Retrocopy LTFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSI-VIDVNKVVEYVQSLQKEDGSFAGDIWGEI

Parental  DTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVN
          DTRFSF.AVATLALLGKLD.INV.KAIEFVLSCMNF.GGFGCRPGSESHAGQIYCCTGFLAITSQLHQVN
Retrocopy DTRFSFSAVATLALLGKLDTINVGKAIEFVLSCMNFVGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVN

Parental  SDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSF-ILACQDEETGGFAD
          SDLLGWWLCE.QLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDR....SF.......E..G.F.D
Retrocopy SDLLGWWLCEQQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDRNCEVSF<LACQDEETGG-FVD

Parental  RPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPEEVLRRVNVQPELVS
          RPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPE.VLRRVNVQP.LVS
Retrocopy RPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPE*VLRRVNVQPKLVS

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	0.17 RPM	31.42 RPM
SRP017611_brain	0.24 RPM	29.30 RPM
SRP017611_kidney	0.73 RPM	97.21 RPM
SRP017611_liver	0.29 RPM	37.92 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2104 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104 ,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851, retro_chof_260,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391, retro_ttru_1767, retro_ttru_214,