RetrogeneDB ID: retro_ptro_1174

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:30018351..30019344(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUFM
• Ensembl ID: ENSPTRG00000007939
• Aliases: None
• Description: Elongation factor Tu [Source:UniProtKB/TrEMBL;Acc:H2QAU9]

Sequence

>retro_ptro_1174
ATGACCACAATGGCGGCTGCCACCTTGCTGCATGCGACGCCTCACTTCAGCGGTCTCGCTGCCGGCCGGACCTTCCTGCT
GCAGGGTCTGTTGCCGCTGCTGAAAGCCCTGGCATTGCCTCTCTTGTGCCGTGGCCTGGCTGTGGGGGCCAAGAAGACTT
AACGTGTGTGAGAAGCCACATGTGAATGTGGGTACCATCAGCCATGTGGACCACGGCAAGACCACGCTGATTGCAGCTAT
CACAAAGATTCTAGCCGAGGGAGGTGGGGCTAAGTTCAAGAAGTACAAGGAGATTGACAATGCCCCCAGAAGAGCAAGCT
CCAGGTATCACCATCAATGCGGCTCATGTGGAGTATAGCACTGTCGCCCACCACTATGCCCACACAGACAGCCCGGGTCA
TGCAGATTATGTTAAGTATATGATCACGGGCACCGCACCCCTCGACGGCTGCCTCCTGGTGGTAGCAGCCAATGACAGCC
CCATGCCCTAGACCCGAGAGCACTTATTACTGGCCAAATAGATTGGGGTGGAGCATGTGGTGGTGTATGTGAACAAGGCT
GATGCTGTCCAGGACTCTGAGATGGTGGAGCTGGTGGAACTGGAGATTCAGGAGCTGTTCACTGAGTTTGGCTATAAAGG
GGAGGAGACCCCAGTCATTGTAGGCTCTGCTGTCTGCCCTTGAGGGTCGGGACCCTGAGTTAGGTCTGAAGTCTGTGCAG
AAGCTACTGGATGCTGTGGACACTTACATCCCAGTGCCCACCCGCGACCTGGAGAAGCCTTTCCTGCTGACTGTAGAGGC
AGTGTACTCCGTGTCTGGCCGTGGCACCATGGTGACAGGTACGCTAGAGCATGACATTTTAAAGAAGGGAGACGAGTGTG
AGCTCCTAGGACATAATAAGAACATCTGCACTGTGCTGACAGGCATTGAGATGTTCCACAAGAGCCTGGAGAGGGCCAAG
GCTGGAGATAACCTCAGGGCCCCGGTCTGAGGG

Alignment

ORF - retro_ptro_1174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 72.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTTMAAATLLRATPHFSGLAAGRTFLLQGLLRLLKAPALPLLCRGLAVEAKKT-YVRDKPHVNVGTIGHV
          MTTMAAATLL.ATPHFSGLAAGRTFLLQGLL.LLKA.ALPLLCRGLAV.AKKT..V..KPHVNVGTI.HV
Retrocopy MTTMAAATLLHATPHFSGLAAGRTFLLQGLLPLLKALALPLLCRGLAVGAKKT>NVCEKPHVNVGTISHV

Parental  DHGKTTLTAAITKILAEGGGAKFKKYEEIDNAP-EERARGITINAAHVEYSTAARHYAHTDCPGHADYVK
          DHGKTTL.AAITKILAEGGGAKFKKY.EIDNAP.EE.A.GITINAAHVEYST.A.HYAHTD.PGHADYVK
Retrocopy DHGKTTLIAAITKILAEGGGAKFKKYKEIDNAP>EEQAPGITINAAHVEYSTVAHHYAHTDSPGHADYVK

Parental  NMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTE
          .MITGTAPLDGC.LVVAAND.PMP.TREHLLLA..IGVEHVVVYVNKADAVQDSEMVELVELEI.EL.TE
Retrocopy YMITGTAPLDGCLLVVAANDSPMP*TREHLLLAK*IGVEHVVVYVNKADAVQDSEMVELVELEIQELFTE

Parental  FGY-KGEETPVIVGSALCALEGRDPELGLKSVQKLLDAVDTYIPVPARDLEKPFLLPVEAVYSVPGRGTV
          FGY.KG...P......L.ALEGRDPELGLKSVQKLLDAVDTYIPVP.RDLEKPFLL.VEAVYSV.GRGT.
Retrocopy FGY>KGRR-PQSL*ALLSALEGRDPELGLKSVQKLLDAVDTYIPVPTRDLEKPFLLTVEAVYSVSGRGTM

Parental  VTGTLERGILKKGDECELLGHSKNIRTVVTGIEMFHKSLERAEAGDNLGALVRG
          VTGTLE..ILKKGDECELLGH.KNI.TV.TGIEMFHKSLERA.AGDNL.A.V.G
Retrocopy VTGTLEHDILKKGDECELLGHNKNICTVLTGIEMFHKSLERAKAGDNLRAPV*G

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	118.29 RPM
SRP007412_cerebellum	0.04 RPM	104.07 RPM
SRP007412_heart	0.00 RPM	136.29 RPM
SRP007412_kidney	0.00 RPM	261.67 RPM
SRP007412_liver	0.00 RPM	225.90 RPM
SRP007412_testis	0.21 RPM	108.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1174 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1174 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1816

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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,