RetrogeneDB ID: retro_ptro_38

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:155857989..155858529(+)
• Located in intron of: ENSPTRG00000012536

Retrocopy information

• Ensembl ID: ENSPTRG00000039444
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000013564
• Aliases: None
• Description: None

Sequence

>retro_ptro_38
ATGGCTTCCCAAAACCGCGACCCAGCCGCCACTAGCGTCGCCGCCGCCCGTAAGGGAGCTGAGCCGAGCGGGGGCGCCGC
CCGGGGTCCGGTGGGCAAAAGGCTACAGCAGGAGCTGATGACCCTCATGATGTCTGGCGATAAAGGGATTTCTGCCTTCC
CTGAATCAGACAACCTTTTCAAATGGGTAGGGACCATCCATGGAGCAGCTGGAACAGTATATGAAGACCTGAGGTATAAG
CTCTCGCTAGAGTTCCCCAGTGGCTACCCTTACAATGCGCCCACAGTGAAGTTCCTCACGCCCTGCTATCACCCCAACGT
GGACACCCAGGGTAACATATGCCTGGACATCCTGAAGGAAAAGTGGTCTGCCCTGTATGACGTCAGGACCATTCTGCTCT
CCATCCAGAGCCTTCTAGGAGAACCCAACATTGATAGTCCCTTGAACACGCATGCTGCCGAGCTCTGGAAAAACCCCACA
GCTTTTAAGAAGTACCTGCAAGAAACCTACTCAAAGCAGGTCACCAGCCAGGAGCCCTGA

Alignment

ORF - retro_ptro_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQNRDPAATSVAAARKGAEPSGGAARGPVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA
          MASQNRDPAATSVAAARKGAEPSGGAARGPVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA
Retrocopy MASQNRDPAATSVAAARKGAEPSGGAARGPVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA

Parental  GTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKEKWSALYDVRTILLSIQSLLG
          GTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKEKWSALYDVRTILLSIQSLLG
Retrocopy GTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKEKWSALYDVRTILLSIQSLLG

Parental  EPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVTSQEP
          EPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVTSQEP
Retrocopy EPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVTSQEP

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	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.50 RPM
SRP007412_heart	0.00 RPM	0.20 RPM
SRP007412_kidney	0.00 RPM	0.24 RPM
SRP007412_liver	0.07 RPM	0.75 RPM
SRP007412_testis	0.00 RPM	0.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_38 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_38 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_38 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 125 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012547	5 retrocopies	retro_amel_1122, retro_amel_1353, retro_amel_157, retro_amel_1621, retro_amel_635,
Bos taurus	ENSBTAG00000016746	1 retrocopy	retro_btau_249,
Canis familiaris	ENSCAFG00000009745	6 retrocopies	retro_cfam_1031, retro_cfam_1805, retro_cfam_1878, retro_cfam_2078, retro_cfam_290, retro_cfam_356,
Choloepus hoffmanni	ENSCHOG00000005054	1 retrocopy	retro_chof_902,
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007, retro_cpor_211,
Dipodomys ordii	ENSDORG00000011774	4 retrocopies	retro_dord_157, retro_dord_386, retro_dord_421, retro_dord_84,
Equus caballus	ENSECAG00000014619	2 retrocopies	retro_ecab_297, retro_ecab_316,
Erinaceus europaeus	ENSEEUG00000010643	14 retrocopies	retro_eeur_113, retro_eeur_177, retro_eeur_249, retro_eeur_253, retro_eeur_266, retro_eeur_272, retro_eeur_294, retro_eeur_346, retro_eeur_375, retro_eeur_518, retro_eeur_592, retro_eeur_604, retro_eeur_641, retro_eeur_80,
Echinops telfairi	ENSETEG00000012346	18 retrocopies	retro_etel_1212, retro_etel_1500, retro_etel_1560, retro_etel_157, retro_etel_1634, retro_etel_1729, retro_etel_1853, retro_etel_1856, retro_etel_2013, retro_etel_221, retro_etel_321, retro_etel_324, retro_etel_400, retro_etel_628, retro_etel_689, retro_etel_764, retro_etel_824, retro_etel_909,
Felis catus	ENSFCAG00000001885	4 retrocopies	retro_fcat_1440, retro_fcat_1530, retro_fcat_1667, retro_fcat_1734,
Homo sapiens	ENSG00000175063	3 retrocopies	retro_hsap_1474, retro_hsap_1922, retro_hsap_2935,
Gorilla gorilla	ENSGGOG00000026061	3 retrocopies	retro_ggor_1130, retro_ggor_1402, retro_ggor_2035,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Microcebus murinus	ENSMICG00000011218	2 retrocopies	retro_mmur_332, retro_mmur_988,
Myotis lucifugus	ENSMLUG00000006715	4 retrocopies	retro_mluc_2164, retro_mluc_2220, retro_mluc_600, retro_mluc_636,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Mus musculus	ENSMUSG00000001403	5 retrocopies	retro_mmus_1344, retro_mmus_1593, retro_mmus_1770, retro_mmus_2881, retro_mmus_3512,
Oryctolagus cuniculus	ENSOCUG00000012176	3 retrocopies	retro_ocun_1005, retro_ocun_1294, retro_ocun_348,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Ochotona princeps	ENSOPRG00000014284	4 retrocopies	retro_opri_1009, retro_opri_1055, retro_opri_222, retro_opri_50,
Pongo abelii	ENSPPYG00000011071	4 retrocopies	retro_pabe_1155, retro_pabe_1221, retro_pabe_1589, retro_pabe_2519,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38 ,
Pteropus vampyrus	ENSPVAG00000000369	1 retrocopy	retro_pvam_423,
Rattus norvegicus	ENSRNOG00000015131	5 retrocopies	retro_rnor_1390, retro_rnor_2131, retro_rnor_2470, retro_rnor_719, retro_rnor_864,
Sarcophilus harrisii	ENSSHAG00000002117	1 retrocopy	retro_shar_832,
Sus scrofa	ENSSSCG00000007423	1 retrocopy	retro_sscr_643,
Tursiops truncatus	ENSTTRG00000015987	1 retrocopy	retro_ttru_1752,