RetrogeneDB ID: retro_oana_124

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra534:791111..791540(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTFDC1
• Ensembl ID: ENSOANG00000009249
• Aliases: None
• Description: replication termination factor 2 domain containing 1 [Source:HGNC Symbol;Acc:15890]

Sequence

>retro_oana_124
GCTTCTTTTCAAGAAGATGATGTCACTGTGCTTGACGATAACAAAGAAGCTGTGGAAATATTAAGAAAAACAATGGAACA
ATGGAAGTTAGAGTCAAAATGAAGATGGGGAAGAAATCAAAGAAACCCAAAGTAACGGAATCAGTTTCTCAACCCCTGCA
GAAGCCCCTTCAGGGCCATCCAAGCTTAAGAGTGATAAGGATGAAATGACCATCAACTCCAAAAAGAAGTATGATTTCTC
CAACAAGAATACAGCAATAACGGGAAATCCTTCAGGAAAACCAATACATCTTCATCCGGATGCTCCGATAGATCCAGAGC
AGAGAGTGAGGAATCAGAGGCATACGGGTCCATTTTCACCACACGCAACTCGGCAAAACGCTCAAAGGAGGAGTCTGCCA
ACTGGATTATTCACATATCATACTGCTTC

Alignment

ORF - retro_oana_124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.67 %
• Parental protein coverage: 51.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAFQEDDVIVLNGSKEDVEIL-RKRMETRRLKMKTGKKSKKP-KATES--VSQPHATEESPGPSKLKSEK
          A.FQEDDV.VL...KE.VEIL..K...T.....K..K..KK..K.T.S...S.....E...GPSKLKS.K
Retrocopy ASFQEDDVTVLDDNKEAVEIL<KKNNGTMEVRVKM-KMGKKS<KETQSNGISFSTPAEAPSGPSKLKSDK

Parental  DEVNINSEKNPSAIPSKEGAAATGNPSGK-ASKSSSGCSKRSIADSDESEAYKSIFTTHSSAKRSKEESS
          DE..INS.K......S....A.TGNPSGK....SSSGCS.RS.A.S.ESEAY.SIFTT..SAKRSKEES.
Retrocopy DEMTINSKKKYDF--SNKNTAITGNPSGK<TNTSSSGCSDRSRAESEESEAYGSIFTTRNSAKRSKEESA

Parental  NWVTHTSYCF
          NW..H.SYCF
Retrocopy NWIIHISYCF

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	94.23 RPM
SRP007412_cerebellum	0.00 RPM	41.52 RPM
SRP007412_heart	0.00 RPM	28.07 RPM
SRP007412_kidney	0.00 RPM	79.06 RPM
SRP007412_liver	0.00 RPM	30.29 RPM
SRP007412_testis	0.00 RPM	65.47 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_124 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_124 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027390	1 retrocopy	retro_btau_1076,
Echinops telfairi	ENSETEG00000003143	1 retrocopy	retro_etel_2095,
Mus musculus	ENSMUSG00000027502	1 retrocopy	retro_mmus_339,
Ornithorhynchus anatinus	ENSOANG00000009249	1 retrocopy	retro_oana_124 ,
Otolemur garnettii	ENSOGAG00000004444	1 retrocopy	retro_ogar_3150,