RetrogeneDB ID: retro_pabe_2002

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:69657245..69658118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHA
• Ensembl ID: ENSPPYG00000003437
• Aliases: None
• Description: L-lactate dehydrogenase A chain [Source:RefSeq peptide;Acc:NP_001126782]

Sequence

>retro_pabe_2002
AGAGGTGCTGGAGCTGTTGCCACCAAGTCCGGGTCTCATTGCCACATGCCCCCGATGCTTGCCTGACATGCATTCCCAAT
TCCTTTTGGTTCCAAGTCCAATATTGCAACTCTTAAGGATCAGCTGATTCATAATCTTCTAAAAGAAGAACAGACCCCCC
CATAAGATTACAGTTGTTGGGGTTTGTGCTGTTGGCATGGTCTGTGCCATCAGTATCTTAACTAAGGACTTGGCAGATGA
ACTTGCTCTTGTTGATGTCATGGAAGACAAATTGAAGGGAGAGATAACGGATCTCCAACATGGCAGCCTTTTCCTTAGAA
CACCAAAGATTATCTCTGGCAAAGACTATAATGTAACTGCAAACTCCAAGCTGGTCATTATCACGTCTAGGGCACGTCAG
CAAGAGGGAGAAAGCCGTCTTAAATAGAACCAGCATAACGTGAACATCTTTAAATTCATCATTCCTAATGTTGTAAAATA
CAGCCCGAACTGCAAGTTGCTTATTGTTTCAAATCCAGTGGATATCTTGACCTATGTGGCTTGGAAGATAAGTGGCTTTC
CCAAAAACCATGTTATTGGAAGTGGTTGCAATCTGGATTCAGCCCAATTCGGTTACCTGATGGGGGAAAGCTGGGAGTTC
ACCCATTAAGCTGTCATGGGCGGGTCCTTGGGGAACATGGAGACTCTAGTGTGCCTTTATGGAATGGAGTCAATGTTGCT
GGTGTTTCCCTGAAGACTCTGCACTCACATTTAGGGACTGATACAGATAAGGAACAGTGGAAAGAGGTTCACAAGCACGT
GGTTGAGAGTCCTTACAAGGTGATCAAACTGAAAGGCTACACATCCTGGGCCATTAGACTCTCACCATTGGAC

Alignment

ORF - retro_pabe_2002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.31 %
• Parental protein coverage: 61.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QSAAAAAADSGSHCHAHPTTARRAFPIPFGSKSNMATLKDQLIHNLLKEEQT-PQNKITVVGVGAVGMAC
          ..A.A.A..SGSHCH..P..A..AFPIPFGSKSN.ATLKDQLIHN.L..E...P..KITVVGV.AVGM.C
Retrocopy RGAGAVATKSGSHCHMPPMLA*HAFPIPFGSKSNIATLKDQLIHN-LLKEEQ>PPHKITVVGVCAVGMVC

Parental  AISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGES
          AISIL.KDLADELALVDV.EDKLKGE..DLQHGSLFLRTPKI.SGKDYNVTANSKLVIIT..ARQQEGES
Retrocopy AISILTKDLADELALVDVMEDKLKGEITDLQHGSLFLRTPKIISGKDYNVTANSKLVIITSRARQQEGES

Parental  RLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMG
          RL...Q.NVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKN.VIGSGCNLDSA.F.YLMG
Retrocopy RLK*NQHNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNHVIGSGCNLDSAQFGYLMG

Parental  E-RLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKL
          E..LGVHPLSCHG.VLGEHGDSSVP.W.G.NVAGVSLKTLH..LGTD.DKEQWKEVHK.VVES.Y.VIKL
Retrocopy E<KLGVHPLSCHGRVLGEHGDSSVPLWNGVNVAGVSLKTLHSHLGTDTDKEQWKEVHKHVVESPYKVIKL

Parental  KGYTSWAIGLSVAD
          KGYTSWAI.LS..D
Retrocopy KGYTSWAIRLSPLD

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	17.97 RPM	88.41 RPM
SRP007412_cerebellum	22.01 RPM	85.49 RPM
SRP007412_heart	9.51 RPM	49.76 RPM
SRP007412_kidney	6.07 RPM	42.20 RPM
SRP007412_liver	21.73 RPM	139.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2002 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2002 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2097
Pan troglodytes	retro_ptro_1540

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 226 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	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pongo abelii	ENSPPYG00000003437	5 retrocopies	retro_pabe_2002 , retro_pabe_2039, retro_pabe_2423, retro_pabe_3407, retro_pabe_364,
Pongo abelii	ENSPPYG00000004356	3 retrocopies	retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,