RetrogeneDB ID: retro_ptro_1059

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:54571642..54572436(-)
• Located in intron of: ENSPTRG00000007109

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000012676
• Aliases: None
• Description: None

Sequence

>retro_ptro_1059
AAGGGCCATGATTCAAAGGAACCAGAGCTTTTGCAAAAACTTTTTATTGGTGGTCTGAGCTTTGAAACTACAGATGATAG
TTAAAGAGACATTTTGAGAAATGGGGCACACTCACAGATTGTGTGGTAATGAGACCCCAAAAAAAACGTTCCAGGGGCTT
TGGTTTTGTGACTTACTCTTGTGTTGAAGAGGTGGAGGCAGCAAGGTGTGCTGGACCACACAAGGCTGATAGGTGTGTAG
TGGAACCAAAGAGAGCTGTTTCTATAGAGGATTCTGTAAAGTCTGGTGCCCATCTAACAGTGAGGAAAATTTTTGTTGGT
TGTATTAAAGAAGAAACAGAAGAATATAATTTGAGAGACTACTTTGAAAAGTATGGCAAGATTGAAATCGCAGAAGTTGT
GGAAGACAGGCAGAGTGGAAAAAAGACAGGATTTGCTTTTATAACTTTTGATGATCATGATACAGTTGATAAAACTGTTG
TTCAGAAATACCACGCTATTAATGGGCATAACTGTGAAGTAAAAAAGGCCCTTTCTAAACAAGAGATGTAGTCTGCTGGA
TGACAGAGATCACAGAGGTAGATCTGGCAATTTTATTATGGAGGAAACTTTGGAGGTGGTAGAGGTAGTTTTGGCTGTGG
TGGAAACTCTGATGGAAGAGGAGGCTATGGTGGTGAAGGTGGTGGCAGCAGAGGTAGTTATGGAGGAGGTGATGGCGGAT
ATAACGGTTTTGGAGGTGATGGTGGCAACTATGGTGGTAGTCCTGGTTACAGTAGTAGAGGGGGCTATGATGGT

Alignment

ORF - retro_ptro_1059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.26 %
• Parental protein coverage: 92.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EGHDPKEPEQLRKLFIGGLSFETTDDS-LREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
          .GHD.KEPE.L.KLFIGGLSFETTDDS.L..HFEKWGTLTDCVVMR.P...RSRGFGFVTYSCVEEV.AA
Retrocopy KGHDSKEPELLQKLFIGGLSFETTDDS<LKRHFEKWGTLTDCVVMR-PXXXRSRGFGFVTYSCVEEVEAA

Parental  MCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
          .CA.PHK.D..VVEPKRAVS.EDSVK.GAHLTV.KIFVG.IKE.TEEYNLRDYFEKYGKIE..EV.EDRQ
Retrocopy RCAGPHKADRCVVEPKRAVSIEDSVKSGAHLTVRKIFVGCIKEETEEYNLRDYFEKYGKIEIAEVVEDRQ

Parental  SGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRG-RGGGSGNFMGR-GGNF
          SGKK.GFAF.TFDDHDTVDK.VVQKYH.INGHNCEVKKALSKQEM.SAG.QR..RG..SGNF....G...
Retrocopy SGKKTGFAFITFDDHDTVDKTVVQKYHAINGHNCEVKKALSKQEM*SAG*QRS>RG-RSGNFIME<GNFG

Parental  GGGGGNFGRGGNFGGRSGNYGGGPGYSSRGGYGGGGPGYGNQGGGYGGGGGYDGYNEGGNFGG
          GG.G..FG.GGN..GR.G...GG.G..SRG.YGGG..GY...GG..G..GG..GY...G...G
Retrocopy GGRG-SFGCGGNSDGRGGY--GGEGGGSRGSYGGGDGGYNGFGGDGGNYGGSPGYSSRGGYDG

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	0.04 RPM	38.32 RPM
SRP007412_cerebellum	0.11 RPM	98.58 RPM
SRP007412_heart	0.00 RPM	55.06 RPM
SRP007412_kidney	0.05 RPM	58.24 RPM
SRP007412_liver	0.03 RPM	85.11 RPM
SRP007412_testis	0.00 RPM	175.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1059 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1059 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1572
Gorilla gorilla	retro_ggor_1197

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059 , retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,