RetrogeneDB ID: retro_ptro_259

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:215035439..215036417(+)
• Located in intron of: ENSPTRG00000002134

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHA
• Ensembl ID: ENSPTRG00000003421
• Aliases: LDHA, LDHC
• Description: Pan troglodytes lactate dehydrogenase A (LDHA), mRNA. [Source:RefSeq mRNA;Acc:NM_001034096]

Sequence

>retro_ptro_259
CTCAAGGATCAGCTTATTCACAGTCTTCTAAAGGAAGAACAGATCCTCCAGAATAAGATTACAGTTGTTGGGGTTGGTGC
TCTTGGCATGGCCTGTGCCATCGGTATCTTAATGAAGGACTTGGCAGGTGAACTTGCTCTTGTTGATGTCATGGAAGACA
AATTGAAGGGCGAGATGATGGATCTCCAACATGGCAGCCTTTTCCTTAGAACACCAAAGATTGTCTCTGGCAAAGACTAT
ACTGTAACTGTAAACTCCAAGCTGGTCACTATCACGGCTGAGGCACATCGCAAGAGGGAGAAAGCCATCTTAATTTGGTC
CTGTGTAATGTGAACATCTTTAAATTCATCATTCCTAATGTTATAAAATACAGCCCGAACTGCAAGTTGCTTATTGTTTC
AAATCCAGTGGATATCTTTGACCTATAGTGGCTTGGAAGATAACGGCTTTCCCAAAAACCATGTTATTGGAAGTGGTTGC
AATCTGGACTCAGCCCAATTCCGTTACCCAATGGGGGAAAGGCTGGGAGTTCACACATTAAGCTGTCATGGGTGAGTCCT
TGGGGAACATGGAGATTCTAGTGTGCCTGTATGGAGTAAAGCGAATGTTACTGGTGTCTCCCTCAAGACTCTGCACCCAG
ATTTAGGGACTGATATAGATAAGGAACAGTGGAAAGAGGTTCACAAGCAGGTGGTCGAGAGTGCTTACGAGGTGATCAAA
CTCAAAGGCTACACATCCTGGGCCACTGGACTCTCTGTGGCAGATTTGGCAGAAAGTATAATGAAGAATCTTAGGCAGGT
GCACCCAATTTCCACCATGATTGGTGGAATAAAGGATGATGTCTTCCTTAGCGTTCCTTGCATCTTGGGAGAGAATGGAA
TCTCAGACCATTTGAAGGTGACTCTGACTCCTGAGGAAGGGGCCCATTTGAAGAACAGTGCAGATCCACTTTGGGGGATA
CAAAAAGAGCTGCAATTT

Alignment

ORF - retro_ptro_259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.19 %
• Parental protein coverage: 99.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKDQLIHNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLR
          LKDQLIH.LLKEEQ..QNKITVVGVGA.GMACAI.ILMKDLA.ELALVDV.EDKLKGEMMDLQHGSLFLR
Retrocopy LKDQLIHSLLKEEQILQNKITVVGVGALGMACAIGILMKDLAGELALVDVMEDKLKGEMMDLQHGSLFLR

Parental  TPKIVSGKDYNVTANSKLVIITAGARQ-QEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDI
          TPKIVSGKDY.VT.NSKLV.ITA.A...QEGES.LNLV..NVNIFKFIIPNV.KYSPNCKLLIVSNPVDI
Retrocopy TPKIVSGKDYTVTVNSKLVTITAEAHR<QEGESHLNLVLCNVNIFKFIIPNVIKYSPNCKLLIVSNPVDI

Parental  -LTY-VAWKIS-GFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGV
          .LTY.VAWKI..GFPKN.VIGSGCNLDSA.FRY.MGERLGVH.LSCHG.VLGEHGDSSVPVWS..NV.GV
Retrocopy >LTY>VAWKIT<GFPKNHVIGSGCNLDSAQFRYPMGERLGVHTLSCHG*VLGEHGDSSVPVWSKANVTGV

Parental  SLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKG
          SLKTLHPDLGTD.DKEQWKEVHKQVVESAYEVIKLKGYTSWA.GLSVADLAESIMKNLR.VHP.STMI.G
Retrocopy SLKTLHPDLGTDIDKEQWKEVHKQVVESAYEVIKLKGYTSWATGLSVADLAESIMKNLRQVHPISTMIGG

Parental  LYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF
          ...IKDDVFLSVPCILG.NGISD..KVTLT.EE.A.LK.SAD.LWGIQKELQF
Retrocopy ---IKDDVFLSVPCILGENGISDHLKVTLTPEEGAHLKNSADPLWGIQKELQF

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	0.05 RPM	183.18 RPM
SRP007412_cerebellum	0.22 RPM	126.72 RPM
SRP007412_heart	0.12 RPM	236.70 RPM
SRP007412_kidney	0.24 RPM	251.34 RPM
SRP007412_liver	0.10 RPM	434.12 RPM
SRP007412_testis	0.00 RPM	259.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_259 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_259 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_323
Pongo abelii	retro_pabe_364

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 223 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017854	2 retrocopies	retro_amel_389, retro_amel_462,
Bos taurus	ENSBTAG00000008683	2 retrocopies	retro_btau_1715, retro_btau_1822,
Choloepus hoffmanni	ENSCHOG00000009977	14 retrocopies	retro_chof_1038, retro_chof_144, retro_chof_1489, retro_chof_1524, retro_chof_1547, retro_chof_172, retro_chof_1874, retro_chof_2121, retro_chof_217, retro_chof_2365, retro_chof_2588, retro_chof_2611, retro_chof_552, retro_chof_990,
Callithrix jacchus	ENSCJAG00000007094	1 retrocopy	retro_cjac_2290,
Cavia porcellus	ENSCPOG00000011926	2 retrocopies	retro_cpor_1055, retro_cpor_427,
Dasypus novemcinctus	ENSDNOG00000018915	11 retrocopies	retro_dnov_1063, retro_dnov_1366, retro_dnov_1429, retro_dnov_1707, retro_dnov_1848, retro_dnov_2417, retro_dnov_362, retro_dnov_669, retro_dnov_797, retro_dnov_821, retro_dnov_887,
Equus caballus	ENSECAG00000020669	5 retrocopies	retro_ecab_1004, retro_ecab_765, retro_ecab_837, retro_ecab_924, retro_ecab_933,
Echinops telfairi	ENSETEG00000007508	15 retrocopies	retro_etel_1091, retro_etel_1192, retro_etel_1243, retro_etel_1309, retro_etel_1439, retro_etel_1609, retro_etel_1870, retro_etel_1916, retro_etel_1969, retro_etel_1996, retro_etel_2209, retro_etel_361, retro_etel_392, retro_etel_828, retro_etel_884,
Homo sapiens	ENSG00000134333	5 retrocopies	retro_hsap_2097, retro_hsap_2285, retro_hsap_3021, retro_hsap_323, retro_hsap_4231,
Gorilla gorilla	ENSGGOG00000010350	3 retrocopies	retro_ggor_1698, retro_ggor_349, retro_ggor_619,
Loxodonta africana	ENSLAFG00000011307	1 retrocopy	retro_lafr_11,
Macropus eugenii	ENSMEUG00000001462	91 retrocopies	retro_meug_101, retro_meug_1029, retro_meug_103, retro_meug_1082, retro_meug_1088, retro_meug_1105, retro_meug_1140, retro_meug_1162, retro_meug_1189, retro_meug_1190, retro_meug_1260, retro_meug_1288, retro_meug_1295, retro_meug_1301, retro_meug_1323, retro_meug_1329, retro_meug_1332, retro_meug_1356, retro_meug_1368, retro_meug_1376, retro_meug_1400, retro_meug_1402, retro_meug_1404, retro_meug_1417, retro_meug_1419, retro_meug_1420, retro_meug_1422, retro_meug_1484, retro_meug_1535, retro_meug_155, retro_meug_1556, retro_meug_1620, retro_meug_1632, retro_meug_1652, retro_meug_1674, retro_meug_1685, retro_meug_1720, retro_meug_1721, retro_meug_1747, retro_meug_1749, retro_meug_1765, retro_meug_1779, retro_meug_1781, retro_meug_181, retro_meug_1824, retro_meug_1875, retro_meug_1898, retro_meug_1906, retro_meug_1915, retro_meug_1927, retro_meug_1945, retro_meug_1977, retro_meug_200, retro_meug_2000, retro_meug_2022, retro_meug_2067, retro_meug_2107, retro_meug_2126, retro_meug_2137, retro_meug_2139, retro_meug_2168, retro_meug_226, retro_meug_244, retro_meug_291, retro_meug_336, retro_meug_351, retro_meug_436, retro_meug_448, retro_meug_477, retro_meug_532, retro_meug_572, retro_meug_590, retro_meug_591, retro_meug_626, retro_meug_634, retro_meug_638, retro_meug_639, retro_meug_660, retro_meug_68, retro_meug_736, retro_meug_737, retro_meug_832, retro_meug_861, retro_meug_867, retro_meug_870, retro_meug_891, retro_meug_916, retro_meug_927, retro_meug_971, retro_meug_980, retro_meug_981,
Macaca mulatta	ENSMMUG00000031024	2 retrocopies	retro_mmul_1037, retro_mmul_587,
Monodelphis domestica	ENSMODG00000006522	2 retrocopies	retro_mdom_161, retro_mdom_206,
Mus musculus	ENSMUSG00000063229	14 retrocopies	retro_mmus_1044, retro_mmus_1300, retro_mmus_1514, retro_mmus_1608, retro_mmus_1753, retro_mmus_1887, retro_mmus_1889, retro_mmus_1925, retro_mmus_2078, retro_mmus_2592, retro_mmus_2885, retro_mmus_3150, retro_mmus_3694, retro_mmus_497,
Nomascus leucogenys	ENSNLEG00000017767	4 retrocopies	retro_nleu_1037, retro_nleu_1303, retro_nleu_1766, retro_nleu_820,
Oryctolagus cuniculus	ENSOCUG00000015939	6 retrocopies	retro_ocun_1597, retro_ocun_1817, retro_ocun_246, retro_ocun_338, retro_ocun_574, retro_ocun_746,
Pongo abelii	ENSPPYG00000003437	5 retrocopies	retro_pabe_2002, retro_pabe_2039, retro_pabe_2423, retro_pabe_3407, retro_pabe_364,
Pan troglodytes	ENSPTRG00000003421	5 retrocopies	retro_ptro_1540, retro_ptro_1618, retro_ptro_2039, retro_ptro_259 , retro_ptro_2875,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Pan troglodytes	ENSPTRG00000004762	1 retrocopy	retro_ptro_3237,
Rattus norvegicus	ENSRNOG00000013009	17 retrocopies	retro_rnor_1131, retro_rnor_1336, retro_rnor_1738, retro_rnor_1769, retro_rnor_1881, retro_rnor_2146, retro_rnor_2377, retro_rnor_2560, retro_rnor_2830, retro_rnor_2950, retro_rnor_2957, retro_rnor_2984, retro_rnor_490, retro_rnor_491, retro_rnor_563, retro_rnor_578, retro_rnor_843,
Sorex araneus	ENSSARG00000001224	1 retrocopy	retro_sara_657,
Sarcophilus harrisii	ENSSHAG00000015776	1 retrocopy	retro_shar_814,
Sus scrofa	ENSSSCG00000013366	1 retrocopy	retro_sscr_12,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,
Tursiops truncatus	ENSTTRG00000013756	2 retrocopies	retro_ttru_1269, retro_ttru_1802,
Vicugna pacos	ENSVPAG00000010215	5 retrocopies	retro_vpac_175, retro_vpac_222, retro_vpac_237, retro_vpac_629, retro_vpac_79,