RetrogeneDB ID: retro_oana_36

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig158946:245..1104(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUFM
• Ensembl ID: ENSOANG00000013114
• Aliases: None
• Description: Tu translation elongation factor, mitochondrial [Source:HGNC Symbol;Acc:12420]

Sequence

>retro_oana_36
GGTATAGCCATCTTATAGACCCAGGTGGAGTATAAAACAGATAAGAGACATTATGGGCATGTAGACTGCCCTGGGCATGC
CCGATTACGTTAAAAATATGATTTCTGGTGCTGCACAAATGGATGGTGCAATTTTGGTGGTTTCAGCGGCCGATGGTCCC
ATGCCCCAAACCAAAGAGCACATTTTGTTAGCCAAACAAATAGGTGTACCCAAAATTGTAGTGTACATGAACAAACTTGA
TATGGTGGAAGACGAAGAATTGTTGGAACTTGTAGAGCTTGAAGTTAGAGAGCTACTAACGGAGCACAAATACGATGGAG
AGTCGGTACCTATCATTAGGGGTTCGGCATTAAAAGCTATCAATGGCGATGTGGATGCTATTGAATCAATAAAATGCCTG
CTTAAAGCGTGCGATGAGTACTTGGCACCGCCGCCCAGACAATCCGACTTACCATTGCTGCTGGCAGTCGATGACGTAAT
GTCAATCCCTGGGAAAGGAACTGTAGCTACTGGACGAATAGAACAGGGCACTCTAAGGCCCGGGGACGCCGTCGAAATAT
ACGGTGGAAGGACCAAGCCCAAACGAAGTGTTTGTGTAAGCCTGGAGATGTTCAGGAAAACATTGTCCGAAGGTATAGCT
GGTGACCAAGTTGGTGTACTCTTGAAAAATATCAAAAAAGACGAGATTTCTCGAGGACACGTCATATCGGCGCCGGGAAA
ATACAAATGCTATGAATGCTTTGATGCAGACGTTTATGTACTAACTCATGAAGAAGGTGGCCGAAAGAACGCCTTCGTTT
CTAATTACCGCCCACAAGCGTTCATTCGGACAGGGGATATCAGTTGCTCCGTTTTACTG

Alignment

ORF - retro_oana_36 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.56 %
• Parental protein coverage: 65.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GITINAAHVEYSTAARHYAHTDCPGHA-DYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLAKQIGV
          GI.I....VEY.T..RHY.H.DCPGHA.DYVKNMI.G.A..DG.ILVV.A.DGPMPQT.EH.LLAKQIGV
Retrocopy GIAIL*TQVEYKTDKRHYGHVDCPGHA>DYVKNMISGAAQMDGAILVVSAADGPMPQTKEHILLAKQIGV

Parental  QHVVVFVNKADAVQDSEMVELVELEIRELLTEFGYNGEKTPVVIGSALCALENREPELGVNSVLKLLDAV
          ...VV..NK.D.V.D.E..ELVELE.RELLTE..Y.GE..P...GSAL.A..N........S...LL.A.
Retrocopy PKIVVYMNKLDMVEDEELLELVELEVRELLTEHKYDGESVPIIRGSALKAI-NGDVD-AIESIKCLLKAC

Parental  DTHIPVPTRDLDKPFLLPLESVYSIPGRGTVVTGTLERGTLKKGDDCE-FLGHGKNLRSVVTGIEMFHKS
          D.....P.R..D.P.LL....V.SIPG.GTV.TG..E.GTL..GD..E...G..K..RSV....EMF.K.
Retrocopy DEYLAPPPRQSDLPLLLAVDDVMSIPGKGTVATGRIEQGTLRPGDAVEIYGGRTKPKRSVCVSLEMFRKT

Parental  LDRAEAGDNLGALVRGLKREDLRRGLVMAKPGSIQPHQKVEAQVYVLSKEEGGRHKPFVSHFMPVMFSLT
          L....AGD..G.L....K.....RG.V...PG.........A.VYVL..EEGGR...FVS...P..F..T
Retrocopy LSEGIAGDQVGVLLKNIKKDEISRGHVISAPGKYKCYECFDADVYVLTHEEGGRKNAFVSNYRPQAFIRT

Parental  WDMACRVIL
          .D..C.V.L
Retrocopy GDISCSVLL

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	0.00 RPM	88.22 RPM
SRP007412_cerebellum	0.00 RPM	78.23 RPM
SRP007412_heart	0.00 RPM	318.01 RPM
SRP007412_kidney	0.00 RPM	82.02 RPM
SRP007412_liver	0.00 RPM	85.98 RPM
SRP007412_testis	0.00 RPM	88.48 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_36 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_36 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,