RetrogeneDB ID: retro_rnor_130

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:30470723..30471521(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000027359
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Slc25a15
• Ensembl ID: ENSRNOG00000011881
• Aliases: Slc25a15, Ab1-114, Ornt1
• Description: mitochondrial ornithine transporter 1 [Source:RefSeq peptide;Acc:NP_001041345]

Sequence

>retro_rnor_130
ATGCAGACATTTCCCTACATGTACAAAGGCCTCGCTGACTGTTTCCTAAAGACATACAACCAAGTGGGTGTCCACGGCCT
TTACAGGGGAACCAGTCCTGCACTGTTAGCCTATGTCGCCCAGGGCTCTGTCCTATTTTTGTGCTATGGCTTTTGCCAAC
AGTTTGTCAGGAAAGTGGCAAGAGTGGAGCAGAGTGCAGAACTGAACGACTTTGAGACTGCCACTGCTGGGTCACTGGCT
TCTGCATTTGCTGCGCTGGTCCTCTGCCCCACTGAGCTTGTGAAGTGTCGGCTGCAGACTATGCATGAAATGAGGGTGGC
AGGGAAGACAAAACACAGCCACAACACAATTTGGTCTATGGTTAAGAGTATCTTCATGAAGGATGGTCCCTTAGGCTTCT
ATCGTGGACTCTCAACCACTCTTGCTCAGGAAATACCTGGATACTTCTTCTACTTTGGGGGCTATGAAATCAGTCGATCA
TTTTTTGCGTCAGGGGGATCAAAGGATGAACTAGGTCCTGTCCCTTTGATGTTAAGTGGAAGCTTTGCTGGGGTTTGTCT
CTGGCTTATCATATTCCCAGTAGACTGCATTAAATCCAGAATCCAGGTTCTTTCTATGTTTGGGAAGCCTGCAGGATTAA
TTAAAACCTTTATAAATGTTGTGAGAAATGAAGGAATATTAGCCTTGTATTCTGGATTGAAAGCCACTCTGATTCGAGCC
ATCCCTTCCAATGCTGCTCTATTTGTGGTTTATGAATACAGCAGAAAGATGATGATGAATGTGGTAGAAGAATACTGA

Alignment

ORF - retro_rnor_130 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.67 %
• Parental protein coverage: 66.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTFPDLYRGLTDCCLRTYSQVGFRGFYKGTSPALIANIAENSVLFMCYGFCQQVVRKVVGLDRQAKLSD
          MQTFP..Y.GL.DC.L.TY.QVG..G.Y.GTSPAL.A..A..SVLF.CYGFCQQ.VRKV......A.L.D
Retrocopy MQTFPYMYKGLADCFLKTYNQVGVHGLYRGTSPALLAYVAQGSVLFLCYGFCQQFVRKVARVEQSAELND

Parental  LQNAAAGSFASAFAALVLCPTELVKCRLQTMYEMETSGKIAASQNTVWSVVKEIFRKDGPLGFYHGLSST
          ...A.AGS.ASAFAALVLCPTELVKCRLQTM.EM...GK...S.NT.WS.VK.IF.KDGPLGFY.GLS.T
Retrocopy FETATAGSLASAFAALVLCPTELVKCRLQTMHEMRVAGKTKHSHNTIWSMVKSIFMKDGPLGFYRGLSTT

Parental  LLREVPGYFFFFGGYELSRSFFASGRSKDELGPIPLMLSGGFGGICLWLAVYPVDCIKSRIQVLSMTGKQ
          L..E.PGYFF.FGGYE.SRSFFASG.SKDELGP.PLMLSG.F.G.CLWL...PVDCIKSRIQVLSM.GK.
Retrocopy LAQEIPGYFFYFGGYEISRSFFASGGSKDELGPVPLMLSGSFAGVCLWLIIFPVDCIKSRIQVLSMFGKP

Parental  TGLIRTFLSIVKNEG
          .GLI.TF...V.NEG
Retrocopy AGLIKTFINVVRNEG

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	0.43 RPM	3.95 RPM
SRP017611_kidney	1.19 RPM	48.08 RPM
SRP017611_liver	0.81 RPM	95.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_130 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_130 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130 ,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,