RetrogeneDB ID: retro_ptro_1079

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:86382483..86382865(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFT20
• Ensembl ID: ENSPTRG00000008911
• Aliases: None
• Description: intraflagellar transport 20 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:30989]

Sequence

>retro_ptro_1079
CAGGACAGCCTGGGTGAAGCAGGACTGTGTTTTGATGAGCTGAGCAAGCCTGGGTGCGGGACCCTGAGGTTACGTAGCAG
ACCAGGGACCCCAAGGAAGACTGCATGGATTTTGTGGACAAAATCAGCCCATTTCAGAAATAGTTGGTGGTTTAATTGAG
CCTGTGGACCAACTTGCAAAAGCAGCAGAAAATGAGAAGAGGAAGGTAGTTGGTGCTTGGAACTTGCTCCAATTTATGGC
AAAACACAGAGAAACCCAACAGCAACAACTTCTAGCACAAACAGCAGAAGAGAAAATGTGGCTAAAAAGGTGGTGGATTG
AATATGAAGCCTCGTGGAAAGTAGATGCACAGAAGGAAACACATTTATTGGCCAGTTTATTT

Alignment

ORF - retro_ptro_1079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 96.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDILGEAGLHFDELNK-LRVLDPEVTQQTIELKEECKDFVDKIGQFQK-IVGGLIELVDQLAKEAENEKM
          .D.LGEAGL.FDEL.K...V.DPEVT.QT...KE.C.DFVDKI..FQK.IVGGLIE.VDQLAK.AENEK.
Retrocopy QDSLGEAGLCFDELSK<AWVRDPEVT*QTRDPKEDCMDFVDKISPFQK<IVGGLIEPVDQLAKAAENEKR

Parental  KAIGARNLLKSIAKQREAQQQQLQALIAEKKMQLERYRVEYEALCKVEAEQNEFIDQFIF
          K..GA.NLL...AK.RE.QQQQL.A..AE.KM.L.R...EYEA..KV.A..........F
Retrocopy KVVGAWNLLQFMAKHRETQQQQLLAQTAEEKMWLKRWWIEYEASWKVDAQKETHLLASLF

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	16.05 RPM
SRP007412_cerebellum	0.00 RPM	11.76 RPM
SRP007412_heart	0.00 RPM	3.09 RPM
SRP007412_kidney	0.00 RPM	14.64 RPM
SRP007412_liver	0.00 RPM	11.92 RPM
SRP007412_testis	0.11 RPM	63.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1079 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1079 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1079 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1217
Pongo abelii	retro_pabe_1322
Macaca mulatta	retro_mmul_2234

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005111	2 retrocopies	retro_amel_1011, retro_amel_1337,
Bos taurus	ENSBTAG00000008110	1 retrocopy	retro_btau_257,
Cavia porcellus	ENSCPOG00000003153	1 retrocopy	retro_cpor_152,
Echinops telfairi	ENSETEG00000018843	2 retrocopies	retro_etel_1045, retro_etel_1181,
Myotis lucifugus	ENSMLUG00000008709	2 retrocopies	retro_mluc_180, retro_mluc_1924,
Monodelphis domestica	ENSMODG00000019233	1 retrocopy	retro_mdom_681,
Mustela putorius furo	ENSMPUG00000014353	1 retrocopy	retro_mputfur_247,
Mus musculus	ENSMUSG00000001105	1 retrocopy	retro_mmus_3245,
Oryctolagus cuniculus	ENSOCUG00000007773	1 retrocopy	retro_ocun_438,
Otolemur garnettii	ENSOGAG00000003333	2 retrocopies	retro_ogar_1169, retro_ogar_72,
Ochotona princeps	ENSOPRG00000005826	6 retrocopies	retro_opri_110, retro_opri_1185, retro_opri_205, retro_opri_293, retro_opri_375, retro_opri_872,
Pan troglodytes	ENSPTRG00000008911	1 retrocopy	retro_ptro_1079 ,
Sus scrofa	ENSSSCG00000023719	1 retrocopy	retro_sscr_315,
Ictidomys tridecemlineatus	ENSSTOG00000007554	1 retrocopy	retro_itri_713,
Tupaia belangeri	ENSTBEG00000005557	2 retrocopies	retro_tbel_180, retro_tbel_1954,