RetrogeneDB ID: retro_rnor_114

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:46872675..46874325(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000029096
• Aliases: Gykl1, Gk-rs1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Gk
• Ensembl ID: ENSRNOG00000034116
• Aliases: Gk, ASTP, Gyk
• Description: glycerol kinase [Source:RefSeq peptide;Acc:NP_077357]

Sequence

>retro_rnor_114
ATGGCAGACGCTCCGAAAGCGGTTTTGGGGCCGTTGGTAGGGGCAGTGGACCAAGGTACCAGCTCAACACGTTTTTTGGT
TTTCAATCCTCAAACAGCTGAATTACTTTGTCATCATCAAGTGGAAATAGCACAGGAGTTCCCAAGAGAAGGATGGGTGG
AGCAAGACCCAAAGGTAATCCTGCAGTCTGTGTATGAGTGTATAGAGAAAACATGTGAGAAACTTGGACAGCAGAGCATT
GACATTTCCAACATTAAAGCTATTGGTGTCACCAACCAGCGGGAAACGACCATAGTCTGGGACAAGTTCACTGGAGAACC
TCTCTACAACGCTGTGGTGTGGCTTGACCTAAGGACCCAGTCTACTGTGGAGAATCTCAACAAAAGTATTTCAGCAAGCA
ATAACTTCATCAAGATCAAGACAGGCCTTCCAATCAGCACTTACTTCAGTGCAGTAAAACTTCACTGGCTCATTGAGAAT
GTGAAAAACGTGCAAAAGGCTATCGAAGATGGCAGAGCGTTTTTTGGGACGGTAGACTCCTGGCTAATCTGGTGCATGAC
GGGAGGTATCAACGGAGGTGTCCACTGTACAGATGTAAGTAATGCGAGTAGGACCATGCTATTCAACATTCACTCTTTGC
AATGGGATGAAGAGCTCTGCGAGTTTTTTGGAATCCCGATGACCATCCTTCCCAGAATCCGGAGTTCTTCTGAGATCTAT
GGCCTAATGAAAAGTGGGGTGTTGGAAGGTGTGCCGATATCTGGGTGCCTGGGAGACCAGTCTGCTGCTTTGGTGGGACA
ATTGTGCCTCCAGGATGGACAAGCTAAAAGCACATATGGAACAGGCTGTTTCTTACTATGTAACACCGGGCAGAAGTGTG
TAAATTCTGACCACGGCCTTCTGACCACGGTGGCTTACAAGATGGGCAGAGAGGAACCTGTCTATTATGCCCTGGAAGGT
TCTGTAGCCATAGCCGGCGCTGTTGTTAGCTGGTTAAAAAACAATCTTCAAATTATTAAGTCGTCATCGGACATTGAAAA
ACTTGCTGAAAAAGCAGGCACTTCCTATGGCTGTTACTTTGTACCAGCCTTTTCAGGCTTATATGCACCTTATTGGGACC
CCAGTGCAAGAGGGATCATCTGTGGGCTCACTCAGTTCACCAATAAATTCCACATCGCATTTGCTGCATTAGAAGCTGTT
TGCTTCCAAACCCGAGAGATTTTAGATGCCATGAACAGTGATTGTGGAATCCCGCTGACACATTTGCAGGTCGACGGAGG
AATGACCGCAAACAAAATTCTTATGCAACTGCAAGCAGACATTTTGTGCATCCCAGTGATGAAACCTTTCATGCCAGAAA
CAACTGCCCTGGGGGCTGCCATGGCTGCAGGGGCAGCAGAAGGAATTAGGGTGTGGAGTCTGGACCCTAAGGATTTAACA
GGTGTCCAGATGGAGAAGTTCGAACCCCAGATCAATGTCGAGGAAAGTGAAGGGCGTTACTCCACATGGAAGAGAGCTGT
GATGAAGTCAATGGGCTGGGTTTTGACTCAGTCTCCTGATGGTCACGACCCAAGTATTTTCAGGAGTCTGACGCTGGGTT
TTTATATAGTGAGTAGTATGGTGTTATTAATTGGCGCAAGGTACATATAA

Alignment

ORF - retro_rnor_114 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
          MA.A.KAVLGPLVGAVDQGTSSTRFLVFN..TAELL.HHQVEI.QEFPREGWVEQDPK.ILQSVYECIEK
Retrocopy MADAPKAVLGPLVGAVDQGTSSTRFLVFNPQTAELLCHHQVEIAQEFPREGWVEQDPKVILQSVYECIEK

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVEKLSKRIPGNNNFVKSK
          TCEKLGQ..IDISNIKAIGV.NQRETT.VWDK.TGEPLYNAVVWLDLRTQSTVE.L.K.I...NNF.K.K
Retrocopy TCEKLGQQSIDISNIKAIGVTNQRETTIVWDKFTGEPLYNAVVWLDLRTQSTVENLNKSISASNNFIKIK

Parental  TGLPLSTYFSAVKLRWLLDNVKKVQEAVEENRALFGTIDSWLIWSLTGGINGGVHCTDVTNASRTMLFNI
          TGLP.STYFSAVKL.WL..NVK.VQ.A.E..RA.FGT.DSWLIW..TGGINGGVHCTDV.NASRTMLFNI
Retrocopy TGLPISTYFSAVKLHWLIENVKNVQKAIEDGRAFFGTVDSWLIWCMTGGINGGVHCTDVSNASRTMLFNI

Parental  HSLEWDKELCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
          HSL.WD.ELCEFFGIPM.ILP..RSSSEIYGLMK.G.LEGVPISGCLGDQSAALVGQ.C.QDGQAK.TYG
Retrocopy HSLQWDEELCEFFGIPMTILPRIRSSSEIYGLMKSGVLEGVPISGCLGDQSAALVGQLCLQDGQAKSTYG

Parental  TGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
          TGCFLLCNTG.KCV.S.HGLLTTVAYK.GR..PVYYALEGSVAIAGAV..WL..NL.IIKSS..IEKLA.
Retrocopy TGCFLLCNTGQKCVNSDHGLLTTVAYKMGREEPVYYALEGSVAIAGAVVSWLKNNLQIIKSSSDIEKLAE

Parental  EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
          ..GTSYGCYFVPAFSGLYAPYW.PSARGIICGLTQFTNK.HIAFAALEAVCFQTREILDAMN.DCGIPL.
Retrocopy KAGTSYGCYFVPAFSGLYAPYWDPSARGIICGLTQFTNKFHIAFAALEAVCFQTREILDAMNSDCGIPLT

Parental  HLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
          HLQVDGGMT.NKILMQLQADIL.IPV.KP.MPETTALGAAMAAGAAEG..VWSL.P.DL..V.ME.FEPQ
Retrocopy HLQVDGGMTANKILMQLQADILCIPVMKPFMPETTALGAAMAAGAAEGIRVWSLDPKDLTGVQMEKFEPQ

Parental  INAEESEIRYSTWKKAVMKSIGWVTTQSPESGIP
          IN.EESE.RYSTWK.AVMKS.GWV.TQSP....P
Retrocopy INVEESEGRYSTWKRAVMKSMGWVLTQSPDGHDP

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
SRP017611_brain	0.00 RPM	12.15 RPM
SRP017611_kidney	0.00 RPM	226.02 RPM
SRP017611_liver	0.00 RPM	286.63 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_rnor_114 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM422677	46873262	46873564	100	302	0	302
CK469738	46872675	46873452	99.9	764	1	754
CK598131	46872716	46873485	99.9	754	0	740

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_114 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_97

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007633	3 retrocopies	retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Echinops telfairi	ENSETEG00000008279	2 retrocopies	retro_etel_2000, retro_etel_247,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Homo sapiens	ENSG00000198814	4 retrocopies	retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana	ENSLAFG00000007632	1 retrocopy	retro_lafr_30,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Mus musculus	ENSMUSG00000025059	2 retrocopies	retro_mmus_119, retro_mmus_97,
Nomascus leucogenys	ENSNLEG00000010102	2 retrocopies	retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Rattus norvegicus	ENSRNOG00000034116	2 retrocopies	retro_rnor_114 , retro_rnor_34,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Ictidomys tridecemlineatus	ENSSTOG00000008732	1 retrocopy	retro_itri_1436,
Tarsius syrichta	ENSTSYG00000008249	1 retrocopy	retro_tsyr_29,