RetrogeneDB ID: retro_rnor_34

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:13695257..13696922(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000029397
• Aliases: Gk2, Gk-rs2
• 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_34
ATGGCAGACTCCAAGGAAACCCCTGAGGAGCCGTTGGTGGGAGCGGTGGTCCAGGGAACCAACTCCACTCGCTTTCTGGT
TTTCAATCCCAAAACAGCAGAACTAGTCGGCAGTCATCAGGTGGAACTGACACAAGAGTATCCGAAAGAAGGATGGGTGG
AGGAAGATCCCAAGGAAATCCTTCAGTCTGTCTATGAATGCATAGCGAAAACTTGCGAGAAACTTACTGAGGCGAACATT
GATACTTCCAAGATTAAAGCTATCGGCGTGAGTAACCAGCGGGAAACCACTGTGGTCTGGGACAAGTTCACGGGAGAGCC
CCTATACAATGCCGTGGTGTGGCTTGATCTCAGAACCCAGTCTACTGTGGAGAGTCTCAATAAGAAAATCCCAGGGAATA
GCAACTTTGTCAAGTCTAAGACAGGCCTTCCACTTAGCACTTACTTCAGTGCTGTGAAACTGCGGTGGATGCTGGACAAC
CTAAGACCCATTCAAAAGGCTGTTGAGGAAGACAGAGCCCTATTTGGAACCATCGACTCGTGGCTCATCTGGTGTATGAC
CGGAGGAGTCAACGGAGGCATCCACTGTACCGATGTAACAAATGCGAGCAGAACGATGCTTTTCAACATCCACTCTTTGG
AATGGGATAAAGAACTCTGTAAATTTTTTGAAATTCCAATGAGCATCCTCCCAAATGTACGCAGTTCTTCCGAGATCTAC
GGCCAGATGACATCCGGGGCTTTGGAAGGCGTGCCAATATCCGGATGTTTGGGGGATCAGTCTGCTGCTTTAGTGGGACA
AATGTGCTTCCAGGAAGGTCAAGCCAAAAACACGTACGGAACCGGATGTTTTTTACTATGCAATACAGGCCAGAAATGTG
TATTTTCTGAACATGGCCTTCTGACTACAGTGGCTTACAAACTAGGCAAAAATAAGCCAGCTTTTTATGCCTTAGAAGGC
TCTGTTGCTATAGCTGGTGCTGTTATTCGCTGGCTAAGAGACAATTTCGAACTTATAACGTCCTCGGGGGAAGTTGAAGA
TCTTGCAAGAGAGGTAGGCACGGCCTACGGCTGCTACTTTGTCCCAGCCTTTTCTGGGTTGTATGCACCTTACTGGGAAC
CCAGTGCAAGAGGGATAATCTGTGGTCTCACTCAGTTCACCAACAAATGCCATATTGCCTTTGCTGCATTAGAAGCCGTT
TGTTTCCAAACCCGAGAGATTGTGGATGCCATGAACCGCGACTGTGGGATTCCACTCAGTCATTTGCGGGTAGATGGAAG
AATGACCAACAACAAGATTCTCATGCAGCTCCAGGCAGATATTCTGCACATTCCGGTAGTTAAATCTGTTATGCCCGAAA
CCACAGCCCTGGGAGCAGCCATGGCAGCCGGAGCTGCAGAAGGGATAGATGTTTGGAGTATTGAACCCGAAGACTTGTCT
TCAATGTTAATGGAACGATATGAACCACAAATCCAAGCCACAGAGAGTGAAATTCGTTTTTCAACATGGAAGAGAGCAGT
GATGAAGTCAATGGGTTGGGTTACAGCCAAGGATCCTGAAAGTAACGCTAACCCTGTCTTCGCTTGCCTGCCCTTGGGGT
TTTTTATAGTGAGTAGCATGACGTTATTAATTGGAGCAAGGTGTATCTCATACGCTGAAGAATAA

Alignment

ORF - retro_rnor_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.07 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
          MA..K.....PLVGAV.QGT.STRFLVFN.KTAEL...HQVE..QE.P.EGWVE.DPKEILQSVYECI.K
Retrocopy MADSKETPEEPLVGAVVQGTNSTRFLVFNPKTAELVGSHQVELTQEYPKEGWVEEDPKEILQSVYECIAK

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVEKLSKRIPGNNNFVKSK
          TCEKL...NID.S.IKAIGVSNQRETTVVWDK.TGEPLYNAVVWLDLRTQSTVE.L.K.IPGN.NFVKSK
Retrocopy TCEKLTEANIDTSKIKAIGVSNQRETTVVWDKFTGEPLYNAVVWLDLRTQSTVESLNKKIPGNSNFVKSK

Parental  TGLPLSTYFSAVKLRWLLDNVKKVQEAVEENRALFGTIDSWLIWSLTGGINGGVHCTDVTNASRTMLFNI
          TGLPLSTYFSAVKLRW.LDN....Q.AVEE.RALFGTIDSWLIW..TGG.NGG.HCTDVTNASRTMLFNI
Retrocopy TGLPLSTYFSAVKLRWMLDNLRPIQKAVEEDRALFGTIDSWLIWCMTGGVNGGIHCTDVTNASRTMLFNI

Parental  HSLEWDKELCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
          HSLEWDKELC.FF.IPM.ILPNVRSSSEIYG.M..GALEGVPISGCLGDQSAALVGQMCFQ.GQAKNTYG
Retrocopy HSLEWDKELCKFFEIPMSILPNVRSSSEIYGQMTSGALEGVPISGCLGDQSAALVGQMCFQEGQAKNTYG

Parental  TGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
          TGCFLLCNTG.KCVFSEHGLLTTVAYKLG..KP..YALEGSVAIAGAVIRWLRDN...I.SS.E.E.LA.
Retrocopy TGCFLLCNTGQKCVFSEHGLLTTVAYKLGKNKPAFYALEGSVAIAGAVIRWLRDNFELITSSGEVEDLAR

Parental  EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
          EVGT.YGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREI.DAMNRDCGIPLS
Retrocopy EVGTAYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREIVDAMNRDCGIPLS

Parental  HLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
          HL.VDG.MT.NKILMQLQADIL.IPVVK..MPETTALGAAMAAGAAEG..VWS.EPEDLS...MER.EPQ
Retrocopy HLRVDGRMTNNKILMQLQADILHIPVVKSVMPETTALGAAMAAGAAEGIDVWSIEPEDLSSMLMERYEPQ

Parental  INAEESEIRYSTWKKAVMKSIGWVTTQSPES
          I.A.ESEIR.STWK.AVMKS.GWVT...PES
Retrocopy IQATESEIRFSTWKRAVMKSMGWVTAKDPES

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

11 EST(s) were mapped to retro_rnor_34 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CK469007	13695257	13696030	99.7	759	3	747
CK469449	13695261	13695902	99.7	639	1	636
CK469758	13695260	13696046	100	765	0	749
CK469842	13695278	13696085	99.9	792	0	781
CK470008	13695243	13696047	99.2	776	4	756
CK470377	13695199	13695962	99.8	754	2	747
CK471109	13695245	13696020	99.8	764	2	754
CK595161	13695280	13695967	99.8	673	1	662
CK652867	13695229	13695957	99.8	716	0	707
CK653376	13695282	13695939	97.1	630	15	606
CK653481	13695272	13696047	99.5	746	2	730

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_34 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_34 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
Sus scrofa	retro_sscr_59
Canis familiaris	retro_cfam_19

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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,