RetrogeneDB ID: retro_rnor_1134

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:10205554..10206438(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Tufm
• Ensembl ID: ENSRNOG00000018604
• Aliases: None
• Description: Elongation factor Tu, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P85834]

Sequence

>retro_rnor_1134
ATGGCAGCAGCCCCTCTATTACGAGCAACTCCCTGCTACAGCGATCTCTAAGCCAGCCGGACCACATTTCTGTAAAGTCA
GCTGTGGCCGCTGAAGGCCTGGTATCGCCCTTCTTGTGTCATTGCACTAGCTGTGGAGGCCAAGAAGACTTACGTATGAG
ACAAGCCCTATGTGAATGTGGGTACCAACGGGCATGTGGACCATGGCAAGACCACCTTGACCATGGCCATCAGGAAAATT
CTATCTGAAGGAGGTGGGGCTAAGTTCAAGAAGTACAAGTAGTTAGACAATGTCCCAGAGGAGTGAGCTCGGGGTATCAC
CATCAATACAGCCCATGTAGAGAATAGCACTGCTGCCCGACACTATGCCCACACAGACTGCCCTGGTCTTGCAGATTATG
TTAAGAATATGATCACAGCCACTGCCCCTTTGGAAGGCTGCATCTTGGTGGTGGCAGCTAAGGATAGCCCTATGCCCCAG
ACGCGAGAGCACTTACTGCTAGCTAAACAGATCAGGGTAGAGCATGTTGTAGTATATGTGAACAAGGCAGAAACTGACCA
GGACTTGGAAATGATGGAGTTAGTAGACCTGGAGATCTGGGAGCTGCTCTCCCAGTTGGGCTATAAAGGAGAGGAAACCC
CAGTCATTGTAGGGTCGGCTCTGTGTGCCCTTGAGCAATGTGATCCTGAGCTAGGTGTGAAGTCAGTGCAGAAGCTTCTG
GATGCTGTGGACACTTACATCCCAGTACCCACCCGGTACCTGGAGAAGCCCTTTCTGCTCCCTGTACAGGCAGTTTACTC
TATTCCTGGTCTCAGCACAATGGTGACAGGCACACTAGAGCATGGCATTTGGAGAAAGGAAATGAACGTGAGTTGCTGGG
ACAT

Alignment

ORF - retro_rnor_1134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.54 %
• Parental protein coverage: 65.27 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAATLLRATPRFSGLCASPTPFLQGRLRPLKA-PASPFLCR-GLAVEAKKTYVRDKPHVNVGTIGHVDH
          MAAA.LLRATP..S.L.AS.T.FL...L.PLKA...SPFLC...LAVEAKKTYV.DKP.VNVGT.GHVDH
Retrocopy MAAAPLLRATPCYSDL*ASRTTFL*SQLWPLKA<LVSPFLCH>ALAVEAKKTYV*DKPYVNVGTNGHVDH

Parental  GKTTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAARHYAHTDCPGHADYVKNMI
          GKTTLT.AI.KIL.EGGGAKFKKY...DN.PEE.ARGITIN.AHVE.STAARHYAHTDCPG.ADYVKNMI
Retrocopy GKTTLTMAIRKILSEGGGAKFKKYK*LDNVPEE*ARGITINTAHVENSTAARHYAHTDCPGLADYVKNMI

Parental  TGTAPLDGCILVVAANDGPMPQTREHLLLAKQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTEFGY
          T.TAPL.GCILVVAA.D.PMPQTREHLLLAKQI.VEHVVVYVNKA...QD.EM.ELV.LEI.ELL...GY
Retrocopy TATAPLEGCILVVAAKDSPMPQTREHLLLAKQIRVEHVVVYVNKAETDQDLEMMELVDLEIWELLSQLGY

Parental  KGEETPVIVGSALCALEQRDPELGVKSVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTVVTGT
          KGEETPVIVGSALCALEQ.DPELGVKSVQKLLDAVDTYIPVPTR.LEKPFLLPV..VYSIPG..T.VTGT
Retrocopy KGEETPVIVGSALCALEQCDPELGVKSVQKLLDAVDTYIPVPTRYLEKPFLLPVQAVYSIPGLSTMVTGT

Parental  LERGI-LKKGDECELLGH
          LE.GI.L.KG.E.ELLGH
Retrocopy LEHGI<LEKGNERELLGH

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	45.73 RPM
SRP017611_kidney	0.00 RPM	125.47 RPM
SRP017611_liver	0.00 RPM	70.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1134 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1134 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016474	1 retrocopy	retro_dord_278,
Homo sapiens	ENSG00000178952	1 retrocopy	retro_hsap_1816,
Macropus eugenii	ENSMEUG00000011131	1 retrocopy	retro_meug_1783,
Monodelphis domestica	ENSMODG00000015564	1 retrocopy	retro_mdom_384,
Mus musculus	ENSMUSG00000073838	1 retrocopy	retro_mmus_10,
Ornithorhynchus anatinus	ENSOANG00000013114	1 retrocopy	retro_oana_36,
Oryctolagus cuniculus	ENSOCUG00000002683	1 retrocopy	retro_ocun_333,
Pan troglodytes	ENSPTRG00000007939	1 retrocopy	retro_ptro_1174,
Rattus norvegicus	ENSRNOG00000018604	1 retrocopy	retro_rnor_1134 ,
Vicugna pacos	ENSVPAG00000009541	1 retrocopy	retro_vpac_346,
Drosophila melanogaster	FBgn0033184	1 retrocopy	retro_dmel_52,