RetrogeneDB ID: retro_ptro_1939

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:158388017..158388611(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYPL1
• Ensembl ID: ENSPTRG00000019570
• Aliases: None
• Description: synaptophysin-like 1 [Source:HGNC Symbol;Acc:11507]

Sequence

>retro_ptro_1939
CTCAAAGAGCTGCTTGACTTCGATATTCTCCAACAGATCATTTCCATCTGTGCTTTTGCCACTTGTGGAGATTTTAAGGA
CAAAACTGATATTTGAATAAGTTATTCTCCTAAAATTACTGACATTAAAACAATTACTGCTATTTTTTGGTTATCCATTC
AGGTTGAATCAGGCATCATTCCAGTCACCTCCAGATGTAAATGTGTGTGATGTAAATTGGAAAAGTCATGTCTTTATAGG
AGGTTGCTCTTCTTCTGCACAATTCTGTCTTATATTTGTAGTCTTTGTCTTCTTGCATTGCATTTCTGCTCTTCTGCTTT
ATGTTGGTTACATGAACACATATGGGCATAGTGAAAAAAAAAAAAACCTTTCCATAACTGACTTTGTTGCAGCTCTTTTT
GCCACTTTTTGAGGTTAGTGAGCCTTTCAACCTAGGCTAAAGCTCTTACAAATGCTGAAATAGCTACCAGTCACAATAAT
GTTCAGGAACATCTGCCTTGCAATCAGCGAAGAGTAACATGTTCATTTGGCTCTATGACTACCATGGGGTCCCTAAATGG
ATCTGTGATCTTTGGTTTTAGGGAGGAAATGCTT

Alignment

ORF - retro_ptro_1939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.2 %
• Parental protein coverage: 75.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKEPLGFIKVLEWIASIFAFATCGGFKGQTEIQVNCPPAITENKTVTAT-FGYPFRLNEASFQPPPGVNI
          LKE.L.F...L..I.SI.AFATCG.FK..T.I.....P.IT..KT.TA..FGYPFRLN.ASFQ.PP.VN.
Retrocopy LKELLDF-DILQQIISICAFATCGDFKDKTDI*ISYSPKITDIKTITAI>FGYPFRLNQASFQSPPDVNV

Parental  CDVNWKDYVLIGDYSSSAQFYVTFAVFVFLYCIAALLLYVGYTSLYLDS---RKLPMIDFVVTLVAT-FL
          CDVNWK..V.IG..SSSAQF...F.VFVFL.CI.ALLLYVGY...Y..S.....L...DFV..L.AT.FL
Retrocopy CDVNWKSHVFIGGCSSSAQFCLIFVVFVFLHCISALLLYVGYMNTYGHSXXXXXLSITDFVAALFAT<FL

Parental  WLVSTSAWAKALTDIKIATGHNIIDELPPCKKKAVLCYFGSVTSMGSLNVSVIFGFLNMIL
          .LVS.S..AKALT...IAT.HN...E..PC....V.C.FGS.T.MGSLN.SVIFGF....L
Retrocopy RLVSLST*AKALTNAEIATSHNNVQEHLPCNQRRVTCSFGSMTTMGSLNGSVIFGFREEML

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	17.09 RPM
SRP007412_cerebellum	0.00 RPM	7.74 RPM
SRP007412_heart	0.00 RPM	37.72 RPM
SRP007412_kidney	0.00 RPM	83.01 RPM
SRP007412_liver	0.00 RPM	19.05 RPM
SRP007412_testis	0.00 RPM	101.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1939 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1939 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1464
Callithrix jacchus	retro_cjac_1588

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016176	2 retrocopies	retro_cjac_1588, retro_cjac_2483,
Cavia porcellus	ENSCPOG00000009221	1 retrocopy	retro_cpor_239,
Equus caballus	ENSECAG00000009695	1 retrocopy	retro_ecab_340,
Homo sapiens	ENSG00000008282	1 retrocopy	retro_hsap_1817,
Gorilla gorilla	ENSGGOG00000006497	1 retrocopy	retro_ggor_1984,
Myotis lucifugus	ENSMLUG00000014980	3 retrocopies	retro_mluc_1884, retro_mluc_2083, retro_mluc_449,
Macaca mulatta	ENSMMUG00000019593	2 retrocopies	retro_mmul_1251, retro_mmul_1464,
Mus musculus	ENSMUSG00000020570	1 retrocopy	retro_mmus_3470,
Nomascus leucogenys	ENSNLEG00000008861	1 retrocopy	retro_nleu_2720,
Oryctolagus cuniculus	ENSOCUG00000015127	3 retrocopies	retro_ocun_1000, retro_ocun_1569, retro_ocun_331,
Otolemur garnettii	ENSOGAG00000008079	2 retrocopies	retro_ogar_1970, retro_ogar_2520,
Ochotona princeps	ENSOPRG00000006755	2 retrocopies	retro_opri_210, retro_opri_448,
Pongo abelii	ENSPPYG00000018292	1 retrocopy	retro_pabe_2370,
Pan troglodytes	ENSPTRG00000019570	2 retrocopies	retro_ptro_1173, retro_ptro_1939 ,
Rattus norvegicus	ENSRNOG00000009856	2 retrocopies	retro_rnor_2273, retro_rnor_2992,
Sorex araneus	ENSSARG00000013935	1 retrocopy	retro_sara_450,
Ictidomys tridecemlineatus	ENSSTOG00000020871	1 retrocopy	retro_itri_1243,
Tupaia belangeri	ENSTBEG00000009095	2 retrocopies	retro_tbel_2025, retro_tbel_2566,
Tarsius syrichta	ENSTSYG00000013296	2 retrocopies	retro_tsyr_1768, retro_tsyr_775,
Tursiops truncatus	ENSTTRG00000002848	1 retrocopy	retro_ttru_661,