RetrogeneDB ID: retro_ptro_1517

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:40842746..40843931(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSPTRG00000012650
• Aliases: OLA1, GTPBP9
• Description: None

Sequence

>retro_ptro_1517
ATGCCCCCTCAAAAGGGAGGTGATGGAATTAAACCACCGCCAATCATTGGAAGATTTGGAACCTCACTGAAAATTGGTAT
TGTTGGATTGCCAAATGTTGGGAAATCTACTTTCTTCAATGTATTAACCAATAGTCAGGCTTCAGCAGAAAACTTCCCAT
TCTGCACTATTGATCCTAATGAGAGCAGAGTACCTGTGCCAGATGAAAGGTTTGACTTTCTTTGCCAATATCACAACCAG
CAAGCAAAATTCCTGCCTTTCTAAATGTAGTGGATATTGCTGGCCTTGTGAAAGGAGCTCACAATGGGCAGGGCCTGGGG
AATGCTTTTTTATCTCATTTTAGTGCTTGTGATGGCATCTTTCATCTAACACGTGCTTTTGAAGATGATGATATCACACA
TGTTGAAGAAAGTGTAGATTCTATTCGAGATATAGAAATAATACATGAAGAGCTTCAGCTCAAAGATGAGGAATGACTGG
GCCCATTATAGATAAACTAGAAAAGGTGGCTGTGAGAGGAGGAGATAAAAAACTAAAACCCGAATATGATATAATGTGCA
AAGTAAAATCCTGGGTTATAGATCAAAAGAACCTGTTCGCTTCTATCATGATTGGAATGACAAAGAGATTGAAGTGTTGA
ATAAACACTTATTTTTGACTTCAAAACCAATGGTCTACTTGGTTAATCTTTCTGAAAAAGACTACATTAGAAAGAAAAAC
AAATGGCTGATAAAAATTAAAGAGTGGGTGGACAAGTATGACCCAGGTGCCTTGGTCATTCCTTTTAGTGGGGCCTTGGA
ACTCAAGTTGCAAGAATTGAGTGCTGAGGAGAGACAGCAGTATCTGGAAGCGAACATGACACAAAGTGCTTTGCCAAAGA
TCATTAAGGCTGGGTTTGCAGCACTCCAACTAAAATACTTTTTCACTGCAGGCCCAGATGAAGTGTGTGCACGGATCATC
AGGAAAGGGACTAAGGCTCCTCAGGCTGCAGGTAAGATTCACACAGATTTTGAAAAGGGATTCATTATGGCTGAAGTAAT
GAAATATGAAGATTTTAAAGAGGAAGGTTCTGAAAATGCAGTCAAGGCTGCTGGAAAGTACAGACAACAAGGCAGAAATT
ATATTGTTGAAGATGCAGATATTATCTTCTTCAAATTTAACACACCTTAACAACTGAAGAAGAAA

Alignment

ORF - retro_ptro_1517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
          MPP.KGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
Retrocopy MPPQKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER

Parental  FDFLCQYH-KPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDITHVEGSV
          FDFLCQYH..PASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSH.SACDGIFHLTRAFEDDDITHVE.SV
Retrocopy FDFLCQYH<QPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHFSACDGIFHLTRAFEDDDITHVEESV

Parental  DPIRDIEIIHEELQLKDEE-MIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQK-KPVRFYHDWN
          D.IRDIEIIHEELQLKDEE.M.GPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQK..PVRFYHDWN
Retrocopy DSIRDIEIIHEELQLKDEE<MTGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQK<EPVRFYHDWN

Parental  DKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAE
          DKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAE
Retrocopy DKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAE

Parental  ERQKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEV
          ERQ.YLEANMTQSALPKIIKAGFAALQL.YFFTAGPDEV.A..IRKGTKAPQAAGKIHTDFEKGFIMAEV
Retrocopy ERQQYLEANMTQSALPKIIKAGFAALQLKYFFTAGPDEVCARIIRKGTKAPQAAGKIHTDFEKGFIMAEV

Parental  MKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK
          MKYEDFKEEGSENAVKAAGKYRQQGRNYIVED.DIIFFKFNTP.Q.KKK
Retrocopy MKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDADIIFFKFNTP*QLKKK

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	0.14 RPM	60.47 RPM
SRP007412_cerebellum	0.07 RPM	62.52 RPM
SRP007412_heart	0.09 RPM	40.02 RPM
SRP007412_kidney	0.18 RPM	47.49 RPM
SRP007412_liver	0.07 RPM	23.73 RPM
SRP007412_testis	0.32 RPM	85.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1517 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1517 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2593
Gorilla gorilla	retro_ggor_1623
Pongo abelii	retro_pabe_1912

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912, retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517 ,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52, retro_vpac_613,