RetrogeneDB ID: retro_ptro_2540

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:62830635..62831110(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GCSH
• Ensembl ID: ENSPTRG00000008386
• Aliases: None
• Description: None

Sequence

>retro_ptro_2540
ACCCTTCACGCGGCCCTGTCACCCCTCGCGCCCTGCCCGCCGAGGCCCTGGCAGCTGGGGGTGGGCGCTGTTCGGACGCT
GCGCGCGGGACCACCTCTGCTCTGGGTGCGTAAATTCACAGAGAAACATGAATGGATGTCAACAGAAAATGATATTGGAA
CACTGGGAATCAGCAGTTTTGCACAGGAAGCGTTGGGAGATATTGTTTACTGTAGTCTGCCTGAAGTTGGGACAAAAGAA
CAAACAAGATGAGTTTGGTGCTTTGGAAAGTGTGAAAGCTGCTAGTGAACTCTATTCTCCTTTATCAGGAGAAGTAACTT
AAATTAATGAAGCTCTTGGAGAAAATCCAGGACTTGTAAACAAATCTTGTTATGAAGATGGTTGGCTGATCAAGATGACA
CTAAGTAACCCTTCAGAACTAGATGAACTTATGAGTGAAGAAGCATATGAGAGATAGAGAAAATCTATTGAGGAG

Alignment

ORF - retro_ptro_2540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 91.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLRGVPSPASPCPPRPWQLGVGAVRTLRTGPALLSVRKFTEKHEWVTTENGIGTVGISNFAQEALGDVVY
          TL....SP..PCPPRPWQLGVGAVRTLR.GP.LL.VRKFTEKHEW..TEN.IGT.GIS.FAQEALGD.VY
Retrocopy TLHAALSPLAPCPPRPWQLGVGAVRTLRAGPPLLWVRKFTEKHEWMSTENDIGTLGISSFAQEALGDIVY

Parental  CSLPEV-GTKLNKQDEFGALESVKAASELYSPLSGEVTEINEALAENPGLVNKSCYEDGWLIKMTLSNPS
          CSLPEV.G.K.NKQDEFGALESVKAASELYSPLSGEVT.INEAL.ENPGLVNKSCYEDGWLIKMTLSNPS
Retrocopy CSLPEV>GQK-NKQDEFGALESVKAASELYSPLSGEVT*INEALGENPGLVNKSCYEDGWLIKMTLSNPS

Parental  ELDELMSEEAYEKYIKSIEE
          ELDELMSEEAYE...KSIEE
Retrocopy ELDELMSEEAYER*RKSIEE

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	0.02 RPM	13.24 RPM
SRP007412_cerebellum	0.00 RPM	3.23 RPM
SRP007412_heart	0.00 RPM	5.19 RPM
SRP007412_kidney	0.00 RPM	10.30 RPM
SRP007412_liver	0.00 RPM	12.77 RPM
SRP007412_testis	0.32 RPM	2.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2540 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2540 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3121

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 175 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008905	1 retrocopy	retro_acar_75,
Ailuropoda melanoleuca	ENSAMEG00000013959	5 retrocopies	retro_amel_1362, retro_amel_1877, retro_amel_229, retro_amel_432, retro_amel_80,
Bos taurus	ENSBTAG00000006795	8 retrocopies	retro_btau_1128, retro_btau_12, retro_btau_1483, retro_btau_1543, retro_btau_1628, retro_btau_246, retro_btau_265, retro_btau_94,
Canis familiaris	ENSCAFG00000020014	5 retrocopies	retro_cfam_1249, retro_cfam_1543, retro_cfam_358, retro_cfam_618, retro_cfam_732,
Choloepus hoffmanni	ENSCHOG00000002434	37 retrocopies	retro_chof_1011, retro_chof_1019, retro_chof_1123, retro_chof_1213, retro_chof_1324, retro_chof_1410, retro_chof_1482, retro_chof_1550, retro_chof_163, retro_chof_1647, retro_chof_1659, retro_chof_1690, retro_chof_1705, retro_chof_1722, retro_chof_178, retro_chof_1781, retro_chof_1787, retro_chof_219, retro_chof_2264, retro_chof_2289, retro_chof_2319, retro_chof_2412, retro_chof_2466, retro_chof_2494, retro_chof_2632, retro_chof_2657, retro_chof_283, retro_chof_335, retro_chof_361, retro_chof_362, retro_chof_363, retro_chof_419, retro_chof_433, retro_chof_477, retro_chof_597, retro_chof_755, retro_chof_931,
Erinaceus europaeus	ENSEEUG00000009653	2 retrocopies	retro_eeur_189, retro_eeur_231,
Felis catus	ENSFCAG00000013038	8 retrocopies	retro_fcat_1007, retro_fcat_1112, retro_fcat_1294, retro_fcat_1435, retro_fcat_1627, retro_fcat_1920, retro_fcat_215, retro_fcat_354,
Homo sapiens	ENSG00000140905	10 retrocopies	retro_hsap_1079, retro_hsap_1380, retro_hsap_2376, retro_hsap_275, retro_hsap_3308, retro_hsap_3389, retro_hsap_3742, retro_hsap_3837, retro_hsap_4125, retro_hsap_465,
Gorilla gorilla	ENSGGOG00000000232	10 retrocopies	retro_ggor_1073, retro_ggor_1306, retro_ggor_1459, retro_ggor_1742, retro_ggor_1802, retro_ggor_2295, retro_ggor_2584, retro_ggor_2772, retro_ggor_320, retro_ggor_853,
Loxodonta africana	ENSLAFG00000015586	3 retrocopies	retro_lafr_554, retro_lafr_822, retro_lafr_900,
Myotis lucifugus	ENSMLUG00000005783	12 retrocopies	retro_mluc_1151, retro_mluc_1221, retro_mluc_1466, retro_mluc_1538, retro_mluc_1659, retro_mluc_1685, retro_mluc_2089, retro_mluc_2090, retro_mluc_2139, retro_mluc_2314, retro_mluc_2411, retro_mluc_709,
Macaca mulatta	ENSMMUG00000013088	5 retrocopies	retro_mmul_1192, retro_mmul_2202, retro_mmul_661, retro_mmul_840, retro_mmul_960,
Mustela putorius furo	ENSMPUG00000009677	4 retrocopies	retro_mputfur_1434, retro_mputfur_1492, retro_mputfur_349, retro_mputfur_809,
Nomascus leucogenys	ENSNLEG00000026844	1 retrocopy	retro_nleu_365,
Procavia capensis	ENSPCAG00000005820	1 retrocopy	retro_pcap_207,
Pongo abelii	ENSPPYG00000007585	15 retrocopies	retro_pabe_1146, retro_pabe_1147, retro_pabe_2146, retro_pabe_2728, retro_pabe_2785, retro_pabe_3060, retro_pabe_3121, retro_pabe_3288, retro_pabe_3289, retro_pabe_3479, retro_pabe_392, retro_pabe_393, retro_pabe_675, retro_pabe_676, retro_pabe_899,
Pan troglodytes	ENSPTRG00000008386	10 retrocopies	retro_ptro_1738, retro_ptro_2163, retro_ptro_230, retro_ptro_2304, retro_ptro_2381, retro_ptro_2540 , retro_ptro_2613, retro_ptro_2802, retro_ptro_2803, retro_ptro_734,
Sarcophilus harrisii	ENSSHAG00000005529	1 retrocopy	retro_shar_239,
Ictidomys tridecemlineatus	ENSSTOG00000016433	2 retrocopies	retro_itri_31, retro_itri_34,
Tupaia belangeri	ENSTBEG00000000056	27 retrocopies	retro_tbel_1426, retro_tbel_1716, retro_tbel_1766, retro_tbel_1846, retro_tbel_1923, retro_tbel_2026, retro_tbel_2074, retro_tbel_2168, retro_tbel_2315, retro_tbel_2426, retro_tbel_2489, retro_tbel_2515, retro_tbel_2573, retro_tbel_2769, retro_tbel_3007, retro_tbel_3025, retro_tbel_311, retro_tbel_3140, retro_tbel_3458, retro_tbel_3852, retro_tbel_3924, retro_tbel_4173, retro_tbel_4727, retro_tbel_597, retro_tbel_601, retro_tbel_609, retro_tbel_825,
Tursiops truncatus	ENSTTRG00000007992	8 retrocopies	retro_ttru_1052, retro_ttru_128, retro_ttru_1415, retro_ttru_1458, retro_ttru_1778, retro_ttru_211, retro_ttru_310, retro_ttru_795,