RetrogeneDB ID: retro_ptro_1413

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:7712680..7713078(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFRS13A
• Ensembl ID: ENSPTRG00000024234
• Aliases: None
• Description: None

Sequence

>retro_ptro_1413
ATGTCTTGCTACTTGTGTCCCCCTAACACGTCTCTCCTCATCAGGAATGTGGCCGATGACACCAGGTCTGAAGATTTACA
GTGTGAATTTGGTCGTTATGGTCCTATAGTTGATGTGTATGTTCCACTTGATTTCTGCACTCACCGTCCAAGATTTGCTT
ATGGTCAACTTGAGGATGTTTGTGATGCTGAAGATGCTTTACATAATTTGGACAGAAAGTGGATTTGTGGACGGCAGATT
GAAATACAGTTTGTCCAGGGCATTGGAAGACACCAAATCAAATGAAAGCCAAGGAAGGGAGGAATGTGTACAGTTCTTCA
CACTATGATGATTATGACAGATACGGACATTCTAGAAGCTGAAGTTATGAAAGAAGATCAAGAAGTCAGTCTTTTGAT

Alignment

ORF - retro_ptro_1413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.82 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRYLRPPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN
          MS.YL.PPNTSL..RNVADDTRSEDL..EFGRYGPIVDVYVPLDF.T.RPR.FAY.Q.EDV.DAEDALHN
Retrocopy MSCYLCPPNTSLLIRNVADDTRSEDLQCEFGRYGPIVDVYVPLDFCTHRPR-FAYGQLEDVCDAEDALHN

Parental  LDRKWICGRQIEIQFAQ-GDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFD
          LDRKWICGRQIEIQF.Q.G..KTPNQMKAKEGRNVYSSS.YDDYDRY..SRS.SYE.RRSRS.SFD
Retrocopy LDRKWICGRQIEIQFVQ<GHWKTPNQMKAKEGRNVYSSSHYDDYDRYGHSRS*SYE-RRSRSQSFD

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	24.08 RPM
SRP007412_cerebellum	0.00 RPM	60.08 RPM
SRP007412_heart	0.03 RPM	27.57 RPM
SRP007412_kidney	0.03 RPM	34.28 RPM
SRP007412_liver	0.00 RPM	24.06 RPM
SRP007412_testis	1.37 RPM	74.93 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1413 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1413 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1413 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2445
Gorilla gorilla	retro_ggor_1522
Pongo abelii	retro_pabe_1796
Callithrix jacchus	retro_cjac_2595

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Loxodonta africana	ENSLAFG00000026905	1 retrocopy	retro_lafr_148,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mus musculus	ENSMUSG00000028676	5 retrocopies	retro_mmus_1081, retro_mmus_1311, retro_mmus_1814, retro_mmus_3480, retro_mmus_982,
Ochotona princeps	ENSOPRG00000018613	3 retrocopies	retro_opri_1067, retro_opri_295, retro_opri_916,
Pan troglodytes	ENSPTRG00000024234	4 retrocopies	retro_ptro_1295, retro_ptro_1413 , retro_ptro_1986, retro_ptro_918,