RetrogeneDB ID: retro_cfam_19

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:3731283..3732942(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000008864
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GK
• Ensembl ID: ENSCAFG00000013713
• Aliases: None
• Description: glycerol kinase [Source:HGNC Symbol;Acc:4289]

Sequence

>retro_cfam_19
ATGGCAGCCCCAAAGAAAACGGTTGTGGGGCCGTTGGTGGGGGCAGTGGTCCAGGGGACGAATTCCACTCGCTTTCTGGT
TTTCAGTTCAAAAACAGCAGATCTGCTTAGTCACCATCAAGTGGAATTAACAGAAGATTTCCCAAGAGAAGAATGGGTGG
AGCAAGACCCTAAGGAAATTCTTCAGTCTGTTTATGAGTGTATAGAGAGAACATGCCAGAAACTTGCTGAACTGCACATT
GAAGTATCCAACATAAAAGCCACTGGTGTCAGCAATCAGAGGGAAACCACTGTAATCTGGGACAAGTTAACTGGAGAGCC
GTTCTATAATGCTATAGTGTGGCTTGATCTAAGAACCCAGCCTACCCTCGAAAACCTTAGTAAAAAAATTCCAGGAAATA
ATAACTTTGTCAAGTCCGAGACAGGCCTTCCACTTAGCACTTACTTCAGTGCAGTGAAACTTCGTTGGATTCTTGACAAT
GTGAGGCAAGTTCAAAAGGCTGTTGAAGAAGGTAGAGCTCTTTTGGGTACCATTGATTCATGGCTAATCTGGAGTGTGAC
AGGAGGAGTTAATGGAGGTGTCCACTGTACAGATGTAACAAATGCAAGCAGGACGATGCTTTCCAACATCCATTCCTTGG
AATGGGATAAAGAGCTTTGTGACTTTTTTGACATTCCGATGGACATTCTTCGGAATGTATGGAGTTCTTCTGATATCTAT
GGCCGCATAAAAGCTGGGTCTTTGGAAGGTGAGCCAATATCTGGGTGCTTGGGGGACCAGTCTGCTGCATTGGTAGGACA
AATGTGCTTCCAAGAGGGACAGGCCAAAAACACGTACAGCACAGGCCGTTTCTTACTATGTAATACAGGTCATAAGTGTG
TATTTTCTGCACATGGCCTTCTGACCACAGTAGCTTATAAACCAGGCAGAGACAAGCCAGTATGTTATGCTTTAGAAGGT
TCTGTTGGTATAGCTGGTGCTGTTATTCGCTGGTTAAGAGACAATCTTGGAATTATAAACACCTCAGAGGAAATTGAAAC
ACTTGCTAAAGATGTAGGTACTTCTTACGGCTGCTACTTTGTCCCAGCTTTTTCAGGCTTATATGCACCTTTTTGGGAGC
CCAGTGCAAGAGGAATAATCTGTGGTCTCTCTCAGTTTACCAGTAAAAATCATATTGCTTTTGCTGCATTAGAATCTGTT
TGTTTCCAAACCCGAGAGATTTTGGATGCCATGAACTATGACTGTGGAATTCCCCTCAGTCATTTGCAGGTAGATGGAGC
AATGACCAACAACAGAATTCTTATGCAACTACAAGCAGACATTCTGCATATTCCAGTAATAAAGCCCTCTATGCCTGAAA
CAACTGCACTGGGAGCTGCCATGGCAGCAGGAGCTGCAGAAGGGGTGGGCGTTTGGAGTCTTAAACCTGAGGATTTGTCA
GTCATCTTTATGGAACGGTTTGAGCCACAGATCAAGGCCACAGAAAGTGAAATTCGTTATTCTACGTGGAAGAAAGCTGT
GAGGAAGTCGATGGGTTGGGTTACAACTCAGTATCCTGAAAGTGGTGATCCTACTATCTTCTCTTGTCTGCCCTTGGGCT
TTTTTATAGTGAGTAGCATGATAATGTTAATTGGAGCAAGATATATTTCAGGTATATCA

Alignment

ORF - retro_cfam_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAKKAVLGPLVGAVDQGTSSTRFLVFNSRTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
          MAA.KK.V.GPLVGAV.QGT.STRFLVF.S.TA.LLSHHQVE....FPRE.WVEQDPKEILQSVYECIE.
Retrocopy MAAPKKTVVGPLVGAVVQGTNSTRFLVFSSKTADLLSHHQVELTEDFPREEWVEQDPKEILQSVYECIER

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
          TC.KL..L.I..SNIKA.GVSNQRETTV.WDKLTGEP.YNA.VWLDLRTQ.T.ENLSK.IPGNNNFVKS.
Retrocopy TCQKLAELHIEVSNIKATGVSNQRETTVIWDKLTGEPFYNAIVWLDLRTQPTLENLSKKIPGNNNFVKSE

Parental  TGLPLSTYFSAVKLRWLLDNVRKVQKAVEEDRALFGTIDSWLIWSLTGGANGGVHCTDVTNASRTMLFNI
          TGLPLSTYFSAVKLRW.LDNVR.VQKAVEE.RAL.GTIDSWLIWS.TGG.NGGVHCTDVTNASRTML.NI
Retrocopy TGLPLSTYFSAVKLRWILDNVRQVQKAVEEGRALLGTIDSWLIWSVTGGVNGGVHCTDVTNASRTMLSNI

Parental  HSLEWDKELCEFFEIPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGEAKNTYG
          HSLEWDKELC.FF.IPM.IL.NV.SSS.IYG..KAG.LEG.PISGCLGDQSAALVGQMCFQ.G.AKNTY.
Retrocopy HSLEWDKELCDFFDIPMDILRNVWSSSDIYGRIKAGSLEGEPISGCLGDQSAALVGQMCFQEGQAKNTYS

Parental  TGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK
          TG.FLLCNTG.KCVFS.HGLLTTVAYK.GRDKPV.YALEGSV.IAGAVIRWLRDNLGII.TSEEIE.LAK
Retrocopy TGRFLLCNTGHKCVFSAHGLLTTVAYKPGRDKPVCYALEGSVGIAGAVIRWLRDNLGIINTSEEIETLAK

Parental  EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
          .VGTSYGCYFVPAFSGLYAP.WEPSARGIICGL.QFT.K.HIAFAALE.VCFQTREILDAMN.DCGIPLS
Retrocopy DVGTSYGCYFVPAFSGLYAPFWEPSARGIICGLSQFTSKNHIAFAALESVCFQTREILDAMNYDCGIPLS

Parental  HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
          HLQVDG.MTNN.ILMQLQADIL.IPV.KPSMPETTALGAAMAAGAAEGVGVWSL.PEDLS...MERFEPQ
Retrocopy HLQVDGAMTNNRILMQLQADILHIPVIKPSMPETTALGAAMAAGAAEGVGVWSLKPEDLSVIFMERFEPQ

Parental  INAEESEIRYSTWKKAVMKSVGWVTTQSSESGIP
          I.A.ESEIRYSTWKKAV.KS.GWVTTQ..ESG.P
Retrocopy IKATESEIRYSTWKKAVRKSMGWVTTQYPESGDP

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	9.37 RPM
SRP017611_brain	0.00 RPM	8.18 RPM
SRP017611_kidney	0.00 RPM	227.37 RPM
SRP017611_liver	0.00 RPM	102.46 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_19 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_19 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_19 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_70
Callithrix jacchus	retro_cjac_125
Mus musculus	retro_mmus_119
Rattus norvegicus	retro_rnor_34
Sus scrofa	retro_sscr_59

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009161	1 retrocopy	retro_amel_45,
Canis familiaris	ENSCAFG00000013713	1 retrocopy	retro_cfam_19 ,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Equus caballus	ENSECAG00000003599	1 retrocopy	retro_ecab_9,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Myotis lucifugus	ENSMLUG00000001046	2 retrocopies	retro_mluc_151, retro_mluc_853,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,