RetrogeneDB ID: retro_ptro_1665

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:187821179..187821801(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28A
• Ensembl ID: ENSPTRG00000000384
• Aliases: None
• Description: lin-28 homolog A (C. elegans) [Source:HGNC Symbol;Acc:15986]

Sequence

>retro_ptro_1665
ATAGGCTCCGTGTCCACCCAGCAGTTTGCAGGTGGCTGCGCCAAGGCGGCAGAAGAGGCACCCGAGGAGGCGCCGGAGGA
TGCGGCCCGGGCGGCGGACGAGGCTCAGCTGCTGCACGGTGAGGGCATCTGTAAGTGGTTCAACTTGCACATGGGATTCG
GCTTACTGTCCGTGACCGCCCGCGCCGTGGTCGCGCTCGACCCGCCAGTGGACGTCTTTGTGCACCAGAGTAAGCTGCCC
ATGGAAGGCTTCCGGAGCTTGAAGGAGGGTGAAGCAGTGGAATTCACCTTTAAGAAGTCAGCCAAGGGTCTGGAATCCAT
CCGTGTCACCGGACCTGGTGGGGCGTTCCGTATTGGGAGTGAGAGGTAGCCAAAGGGGAAGAACATGCAAGAAGCGCAGA
TCAAAAGACAGGTGCTACAACTGTGGAGGTCTAGACCATCATGCCAAGGAATGCAAGATGCCACCCCAGGCCAAGAAGTG
CCACTTCTGCCAGAGCATCAGTCATATGGTAGCTTCATGTCCACTGAAGGCCCAGCAGGGCCCTAGCGCACAGGGAAAGC
CAACGTACTTTCAGGAGGAAGAAGAAATCCACAGCCCTGCCCTGCTCCCGGAGGCGCAGAAT

Alignment

ORF - retro_ptro_1665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSVSNQQFAGGCAKAAEEAPEEAPEDAARAADEPQLLHGAGICKWFNVRMGFGFLCMTARAGVALDPPV
          .GSVS.QQFAGGCAKAAEEAPEEAPEDAARAADE.QLLHG.GICKWFN..MGFG.L..TARA.VALDPPV
Retrocopy IGSVSTQQFAGGCAKAAEEAPEEAPEDAARAADEAQLLHGEGICKWFNLHMGFGLLSVTARAVVALDPPV

Parental  DVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKGKNMQ-KRRSKGDRC
          DVFVHQSKL.MEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGG.F.IGSER.PKGKNMQ.KRRSK.DRC
Retrocopy DVFVHQSKLPMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGAFRIGSER*PKGKNMQ>KRRSK-DRC

Parental  YNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQGKPTYFREEEEEIHSPTLLPEAQN
          YNCGGLDHHAKECK.PPQ.KKCHFCQSISHMVASCPLKAQQGPSAQGKPTYF..EEEEIHSP.LLPEAQN
Retrocopy YNCGGLDHHAKECKMPPQAKKCHFCQSISHMVASCPLKAQQGPSAQGKPTYF-QEEEEIHSPALLPEAQN

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	0.11 RPM	0.00 RPM
SRP007412_cerebellum	0.18 RPM	0.04 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.05 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.11 RPM	1.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1665 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1665 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2187
Gorilla gorilla	retro_ggor_1732
Pongo abelii	retro_pabe_2067

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010582	2 retrocopies	retro_amel_396, retro_amel_649,
Bos taurus	ENSBTAG00000040497	3 retrocopies	retro_btau_1150, retro_btau_1594, retro_btau_199,
Canis familiaris	ENSCAFG00000012488	2 retrocopies	retro_cfam_2049, retro_cfam_767,
Callithrix jacchus	ENSCJAG00000009796	5 retrocopies	retro_cjac_1468, retro_cjac_1784, retro_cjac_186, retro_cjac_2597, retro_cjac_33,
Cavia porcellus	ENSCPOG00000019646	1 retrocopy	retro_cpor_120,
Dasypus novemcinctus	ENSDNOG00000010710	5 retrocopies	retro_dnov_102, retro_dnov_1112, retro_dnov_2300, retro_dnov_690, retro_dnov_853,
Equus caballus	ENSECAG00000020267	1 retrocopy	retro_ecab_258,
Homo sapiens	ENSG00000131914	2 retrocopies	retro_hsap_2187, retro_hsap_2450,
Gorilla gorilla	ENSGGOG00000024918	2 retrocopies	retro_ggor_1526, retro_ggor_1732,
Myotis lucifugus	ENSMLUG00000010158	1 retrocopy	retro_mluc_1023,
Nomascus leucogenys	ENSNLEG00000009294	4 retrocopies	retro_nleu_204, retro_nleu_2300, retro_nleu_2896, retro_nleu_316,
Oryctolagus cuniculus	ENSOCUG00000000299	1 retrocopy	retro_ocun_19,
Otolemur garnettii	ENSOGAG00000003971	1 retrocopy	retro_ogar_481,
Pongo abelii	ENSPPYG00000001684	3 retrocopies	retro_pabe_1801, retro_pabe_2067, retro_pabe_2849,
Pan troglodytes	ENSPTRG00000000384	2 retrocopies	retro_ptro_1415, retro_ptro_1665 ,
Pteropus vampyrus	ENSPVAG00000017267	1 retrocopy	retro_pvam_110,
Rattus norvegicus	ENSRNOG00000038409	2 retrocopies	retro_rnor_2076, retro_rnor_2077,
Sus scrofa	ENSSSCG00000003557	1 retrocopy	retro_sscr_358,
Ictidomys tridecemlineatus	ENSSTOG00000004329	1 retrocopy	retro_itri_1647,
Tursiops truncatus	ENSTTRG00000005678	4 retrocopies	retro_ttru_1312, retro_ttru_1559, retro_ttru_481, retro_ttru_548,