RetrogeneDB ID: retro_itri_964

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393351.1:1102880..1103327(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SC5D
• Ensembl ID: ENSSTOG00000008946
• Aliases: None
• Description: sterol-C5-desaturase [Source:HGNC Symbol;Acc:10547]

Sequence

>retro_itri_964
TCTTTGGGACTCCTGATTTTAATAAATCTTAGTGCTTATATCCTTTATTTCTTCTGTGAAAAATTGAGCTACTGTTTTGT
ATATGATCATTCACTGATGAATTATCCATAGTTTTAAAGAATCAAGTGTATTGAGAGATGAAGGTTATTGTTCAGTCAGT
ACCATGGGTAAGGATCCTCACCATTTCATTGTTCCTGCTGAAATTGAGAGGGTACAGTAATTTTATGGAAACATGGGACA
GTTTACAAATAGCTGGTTTTAACTCACTGTTAGTATAATATCCTCCCTCTTTTTCACCAACATGTTGAACTGCTGAATTC
ACAGAGGCCTTCTACATAGACTTGTATAAAAGCACACAGTAGAACTCACCATATTTGGAAGATTCTCACTCCATTTGTAT
GCAAATACATCCCAGTGAAAGCTTCCCTTCAGAATCTACTTTACCAC

Alignment

ORF - retro_itri_964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.39 %
• Parental protein coverage: 50.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TISLLIVTNLGAYILYFFCATLSYYFVYDHSLMKHPQF-LKNQVYREIKFTVQSLPWISIPTVALFLLEL
          ...LLI..NL.AYILYFFC..LSY.FVYDHSLM..P.F.LKNQVY.E.K..VQS.PW..I.T..LFLL.L
Retrocopy SLGLLILINLSAYILYFFCEKLSYCFVYDHSLMNYP*F<LKNQVY*EMKVIVQSVPWVRILTISLFLLKL

Parental  RGYSK-LYDNIGEFPSGWFHLIVSVISFLFFTDMLIYWIHRGLHHRLV-YKRIHKPHHIWKIPTPFASHA
          RGYS...Y.N.G.F...WF.L.VS.IS.LFFT.ML...IHRGL.HRLV..K.....HHIWKI.TPF....
Retrocopy RGYSN<FYGNMGQFTNSWF*LTVSIISSLFFTNMLNC*IHRGLLHRLV<IKAHSRTHHIWKILTPFVC-K

Parental  FHPVDGFLQSLPYH
          ..PV...LQ.L.YH
Retrocopy YIPVKASLQNLLYH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_964 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_964 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019246	1 retrocopy	retro_btau_813,
Canis familiaris	ENSCAFG00000011805	1 retrocopy	retro_cfam_291,
Callithrix jacchus	ENSCJAG00000007436	1 retrocopy	retro_cjac_1911,
Monodelphis domestica	ENSMODG00000013028	1 retrocopy	retro_mdom_1086,
Mustela putorius furo	ENSMPUG00000005754	1 retrocopy	retro_mputfur_484,
Ochotona princeps	ENSOPRG00000003219	1 retrocopy	retro_opri_1143,
Ictidomys tridecemlineatus	ENSSTOG00000008946	1 retrocopy	retro_itri_964 ,
Tupaia belangeri	ENSTBEG00000000490	1 retrocopy	retro_tbel_4326,
Tarsius syrichta	ENSTSYG00000011139	1 retrocopy	retro_tsyr_1097,
Tursiops truncatus	ENSTTRG00000006908	1 retrocopy	retro_ttru_777,