RetrogeneDB ID: retro_ptro_1023

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:64715050..64715439(+)
• Located in intron of: ENSPTRG00000007202

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSPTRG00000002666
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_ptro_1023
ATGAATGACATGGTAACTATCCAAACTGGAAAGTTCATGACCAACCAACTACTTCAGTGAAAACAAATGGTCATTGATGT
CCTTCACCCTGGGAAGGCAACACTGCCTAAGAGAGAAATTCAGGAAAAAGTAGCCAAAATGTACAAGACCACACCAGATG
TCATCTTTGAGTTCAGAACTCATTTTGGTGGTGGCAAGACTACTGGCTTTGGCATAATTTACGATTCCTTGGATTATGCA
AACAAAAATGAACACAAACATAGACTTACAAGACATGGCCTGTGTGAGAAGAAAAAGACCTTGAGAAAGCAATGAAAGGA
ATGTAAGAACAGCATGAAGAAGGTAGGCAGACAGCAAAGGCCAGTGTTAGTGCTGGCAAAAAGCCAAAG

Alignment

ORF - retro_ptro_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
          MND.VTI.T.KFMTN.LLQ.KQMVIDVLHPGKAT.PK.EI.EK.AKMYKTTPDVIF...FRTHFGGGKTT
Retrocopy MNDMVTIQTGKFMTNQLLQ*KQMVIDVLHPGKATLPKREIQEKVAKMYKTTPDVIFE--FRTHFGGGKTT

Parental  GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKV-RGTAKANVGAGKKQK
          GFG.IYDSLDYA.KNE.KHRL.RHGL.EKKKT.RKQ.KE.KN.MKKV.R.TAKA.V.AGKK.K
Retrocopy GFGIIYDSLDYANKNEHKHRLTRHGLCEKKKTLRKQ*KECKNSMKKV<RQTAKASVSAGKKPK

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	0.07 RPM	165.41 RPM
SRP007412_cerebellum	0.04 RPM	121.81 RPM
SRP007412_heart	0.00 RPM	107.14 RPM
SRP007412_kidney	0.03 RPM	169.33 RPM
SRP007412_liver	0.00 RPM	135.09 RPM
SRP007412_testis	0.00 RPM	76.82 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1023 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1023 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1511

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013264	9 retrocopies	retro_btau_1137, retro_btau_1311, retro_btau_1562, retro_btau_285, retro_btau_467, retro_btau_577, retro_btau_586, retro_btau_788, retro_btau_980,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Homo sapiens	ENSG00000138326	3 retrocopies	retro_hsap_1511, retro_hsap_526, retro_hsap_658,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pan troglodytes	ENSPTRG00000002666	10 retrocopies	retro_ptro_1023 , retro_ptro_1114, retro_ptro_1257, retro_ptro_1555, retro_ptro_1885, retro_ptro_2376, retro_ptro_362, retro_ptro_393, retro_ptro_478, retro_ptro_983,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728,