RetrogeneDB ID: retro_oana_90

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig62566:1437..2607(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHA
• Ensembl ID: ENSOANG00000010157
• Aliases: None
• Description: succinate dehydrogenase complex, subunit A, flavoprotein (Fp) [Source:HGNC Symbol;Acc:10680]

Sequence

>retro_oana_90
ACGGCATGTGTTACAAAGTTGTTTCCAACAAGATCCCACACGGTTGCAGCCCAGGGTGGCATCAATGCTGCCTTGGGAAA
CATGTGCGAGGACGATTGGCGGTGGCATGCATATGATACTGTAAAAGGGTCAGATTGGTTAGGGGATCAAGATGCAATCC
ACTACATGTGCAAAAGCGCCCCTGAGGCTGTGATAGAGTTGGAAAACTACGGGCTGCCGTTCTCGCGAACTGCCCAAGGC
ACCATCTACCAACGAGCTTTTGGGGGTCAATCCCTCAAATACGGCAAAGGCGGTCAAGCGTACCGCTGCGCAGCAGCCGC
AGATCGTACCGGTCATGCTATGCTGCATACGTTGTATGGTCAAGCGCTAGCGCATGAGTGCAAGTTTTTTGTTGAGTATT
TTTTATTGGAGCTAGTTCGTGACTCGCAAACAAACCAAACCAAAGGTGTGTTGTGTTGGAATATCGCCAATGGAGACTTA
CACGCGTTTCATGCGCGTCATGTTGTAATGTGTACGGGTGGATTTGGGCGTTGTTATTTGAGTTGCACTAGTGCTCACAT
GTGCACTGGTGATGGCAACGCTGCAGTGTCGAGGTTGGGTTTACCACTGCAAGATATGGAGTTTGTTCAGTTTCATCCCA
CTGGGATTTATCCAGCTGGGTGTCTTATAACGGAAGGATGCCGTGGCGAAGGTGGTGTATTGAGAAACGCCGAAGGTGAA
GCATTCATGGGCAGGTATGCCCCTGTCGCCAAGGACTTGGCAAGTAGAGACGTAGTCTCGAGGGCAATGACACTCGAAAT
CAACGCCGGTAGAGGCTGTGGTCCCCAAAAGGACCATTTGTATTTGGATTTGACTCATCTTGATGATGAAACATTCAAAG
AAAAACTCCCTGGTATAACAGAAACGGCCAAAATCTTCGCCGGTGTAGACGCCCGTAAAGATTACATTCCAGTGTTACCC
ACTGTGCATTACAATATGGGTGGCATTCCTACAAACTGGAAATCCCAAGTTTTGGACCGCCGCAACAACAAGGATGTTAT
TGTTGAGGGGCTCTACGCAGCTGGTGAAGCTGCGTGCGCTTCGGTTCACGGCGCTAACAGACTTGGAGCTAATTCGCTTT
TGGATATTGTGGTTTTTGGAAAGAGGGCCGCTTTAACCATAAAAGAAACA

Alignment

ORF - retro_oana_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 59.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TACLTKLFPTRSHTVAAQGGINAALGNMEEDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPASVVELENY
          TAC.TKLFPTRSHTVAAQGGINAALGNM.ED.WRWH.YDTVKGSDWLGDQDAIHYM...AP..V.ELENY
Retrocopy TACVTKLFPTRSHTVAAQGGINAALGNMCEDDWRWHAYDTVKGSDWLGDQDAIHYMCKSAPEAVIELENY

Parental  GMPFSRTEEGKIYQRAFGGQSLQFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLM
          G.PFSRT..G.IYQRAFGGQSL..GKGGQA.RC...ADRTGH..LHTLYG..L......FVEYF.L.L..
Retrocopy GLPFSRTAQGTIYQRAFGGQSLKYGKGGQAYRCAAAADRTGHAMLHTLYGQALAHECKFFVEYFLLELVR

Parental  EN--GECRGVIALCIEDGSIHRIRAKNTVVATGGYGRTFFSCTSAHTSTGDGTAMITRAGLPCQDLEFVQ
          ........GV....I..G..H...A...V..TGG.GR...SCTSAH..TGDG.A...R.GLP.QD.EFVQ
Retrocopy DSQTNQTKGVLCWNIANGDLHAFHARHVVMCTGGFGRCYLSCTSAHMCTGDGNAAVSRLGLPLQDMEFVQ

Parental  FHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTIEIREGRGCGPEKDHV
          FHPTGIY.AGCLITEGCRGEGG.L.N..GE.FM.RYAPVAKDLASRDVVSR.MT.EI..GRGCGP.KDH.
Retrocopy FHPTGIYPAGCLITEGCRGEGGVLRNAEGEAFMGRYAPVAKDLASRDVVSRAMTLEINAGRGCGPQKDHL

Parental  YLQLHHLPPEQLASRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVLKHVNGKDQVVPG
          YL.L.HL..E.....LPGI.ETA.IFAGVD..K..IPVLPTVHYNMGGIPTN.K.QVL...N.KD..V.G
Retrocopy YLDLTHLDDETFKEKLPGITETAKIFAGVDARKDYIPVLPTVHYNMGGIPTNWKSQVLDRRNNKDVIVEG

Parental  LYACGEAASASVHGANRLGANSLLDLVVFGRACALSIAES
          LYA.GEAA.ASVHGANRLGANSLLD.VVFG...AL.I.E.
Retrocopy LYAAGEAACASVHGANRLGANSLLDIVVFGKRAALTIKET

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	1060.27 RPM
SRP007412_cerebellum	0.00 RPM	724.88 RPM
SRP007412_heart	0.09 RPM	1014.95 RPM
SRP007412_kidney	0.00 RPM	1453.53 RPM
SRP007412_liver	0.00 RPM	1016.43 RPM
SRP007412_testis	0.00 RPM	267.33 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_90 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_90 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000001292	1 retrocopy	retro_nleu_2643,
Ornithorhynchus anatinus	ENSOANG00000010157	1 retrocopy	retro_oana_90 ,
Xenopus tropicalis	ENSXETG00000023408	1 retrocopy	retro_xtro_61,
Drosophila melanogaster	FBgn0261439	1 retrocopy	retro_dmel_7,