RetrogeneDB ID: retro_pabe_404

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:82208227..82208691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL29
• Ensembl ID: ENSPPYG00000013818
• Aliases: None
• Description: ribosomal protein L29 [Source:HGNC Symbol;Acc:10331]

Sequence

>retro_pabe_404
ATGGCCAAGTCCAAGAACCACACCACATGCAACCAGTCCCGAAAATGGCACAGAAATGGCATCAAGAAACCTCGATTGCA
AAGATATGAATCTCTTAAGGGGTGGACCCCAGGTTCCTGAGGAACATGGGCTTTGCCAAGAAGTGCAAGAAGAAGGGCCT
AAAGAAGATGCAGGCCAACAATGCCAAGGCCATGAGTGCACGTGCTGAGGCTATCAAGGCCCTCATAAAGCCAAAGGAGG
TTAAGCCTAAGATGCCAAAGGGTGTCAGCCACAACCTCAGTCAATTTGCATACATTACCCACCCCAAGCTTGGGAAGCGT
GCTTGTGCCCGCATTGCCAAGGGGCTCAGGTTGTGTGGGCCAAAGGCCAAAGCCAAGGATCAAACCAAGGCCCAGGCTGC
AGCTCCAGCTTCAGTTTCAGCTCAGGCTCCCAAAGATGCCCAGGCCCCTACAAGGACTTCAGAG

Alignment

ORF - retro_pabe_404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKG-VDPKFLRNMRFAKKHNKKGLKKMQANNAKAMSARA
          MAKSKNHTT.NQSRKWHRNGIKKPR.QRYESLKG.VDP.FLRNM.FAKK..KKGLKKMQANNAKAMSARA
Retrocopy MAKSKNHTTCNQSRKWHRNGIKKPRLQRYESLKG<VDPRFLRNMGFAKKCKKKGLKKMQANNAKAMSARA

Parental  EAIKALVKPKEVKPKIPKGVSRKLDRLAYIAHPKLGKRARARIAKGLRLCRPKAKAKDQTKAQAAAPASV
          EAIKAL.KPKEVKPK.PKGVS..L...AYI.HPKLGKRA.ARIAKGLRLC.PKAKAKDQTKAQAAAPASV
Retrocopy EAIKALIKPKEVKPKMPKGVSHNLSQFAYITHPKLGKRACARIAKGLRLCGPKAKAKDQTKAQAAAPASV

Parental  PAQAPKGAQAPTKASE
          .AQAPK.AQAPT..SE
Retrocopy SAQAPKDAQAPTRTSE

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	73.76 RPM
SRP007412_cerebellum	0.00 RPM	64.57 RPM
SRP007412_heart	0.00 RPM	102.41 RPM
SRP007412_kidney	0.17 RPM	190.89 RPM
SRP007412_liver	0.00 RPM	203.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_404 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_404 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_263
Gorilla gorilla	retro_ggor_312

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 247 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009163	6 retrocopies	retro_amel_1373, retro_amel_1740, retro_amel_345, retro_amel_379, retro_amel_686, retro_amel_913,
Bos taurus	ENSBTAG00000018628	1 retrocopy	retro_btau_982,
Callithrix jacchus	ENSCJAG00000005951	9 retrocopies	retro_cjac_135, retro_cjac_160, retro_cjac_241, retro_cjac_29, retro_cjac_331, retro_cjac_348, retro_cjac_358, retro_cjac_73, retro_cjac_96,
Cavia porcellus	ENSCPOG00000011738	1 retrocopy	retro_cpor_1509,
Dasypus novemcinctus	ENSDNOG00000000209	7 retrocopies	retro_dnov_1743, retro_dnov_1900, retro_dnov_1923, retro_dnov_1952, retro_dnov_2050, retro_dnov_2163, retro_dnov_2614,
Equus caballus	ENSECAG00000007397	2 retrocopies	retro_ecab_766, retro_ecab_904,
Felis catus	ENSFCAG00000001762	9 retrocopies	retro_fcat_1032, retro_fcat_1132, retro_fcat_1753, retro_fcat_1774, retro_fcat_1897, retro_fcat_249, retro_fcat_485, retro_fcat_687, retro_fcat_952,
Homo sapiens	ENSG00000162244	23 retrocopies	retro_hsap_1098, retro_hsap_1146, retro_hsap_123, retro_hsap_1283, retro_hsap_1406, retro_hsap_1587, retro_hsap_170, retro_hsap_1759, retro_hsap_2053, retro_hsap_2358, retro_hsap_263, retro_hsap_2772, retro_hsap_2899, retro_hsap_3201, retro_hsap_3289, retro_hsap_3316, retro_hsap_3511, retro_hsap_3562, retro_hsap_3951, retro_hsap_3998, retro_hsap_4304, retro_hsap_863, retro_hsap_882,
Gorilla gorilla	ENSGGOG00000024691	16 retrocopies	retro_ggor_1007, retro_ggor_1090, retro_ggor_1205, retro_ggor_1315, retro_ggor_1330, retro_ggor_142, retro_ggor_1480, retro_ggor_1929, retro_ggor_224, retro_ggor_2247, retro_ggor_254, retro_ggor_2684, retro_ggor_312, retro_ggor_715, retro_ggor_863, retro_ggor_892,
Loxodonta africana	ENSLAFG00000005757	5 retrocopies	retro_lafr_164, retro_lafr_184, retro_lafr_257, retro_lafr_461, retro_lafr_831,
Microcebus murinus	ENSMICG00000002705	9 retrocopies	retro_mmur_192, retro_mmur_198, retro_mmur_303, retro_mmur_446, retro_mmur_508, retro_mmur_519, retro_mmur_657, retro_mmur_816, retro_mmur_938,
Myotis lucifugus	ENSMLUG00000015088	14 retrocopies	retro_mluc_1086, retro_mluc_1160, retro_mluc_134, retro_mluc_1377, retro_mluc_1699, retro_mluc_1955, retro_mluc_2228, retro_mluc_2522, retro_mluc_2523, retro_mluc_2575, retro_mluc_297, retro_mluc_421, retro_mluc_889, retro_mluc_915,
Macaca mulatta	ENSMMUG00000019248	2 retrocopies	retro_mmul_1352, retro_mmul_218,
Monodelphis domestica	ENSMODG00000028750	17 retrocopies	retro_mdom_1013, retro_mdom_1187, retro_mdom_1201, retro_mdom_1328, retro_mdom_1445, retro_mdom_1452, retro_mdom_1505, retro_mdom_1532, retro_mdom_1604, retro_mdom_1665, retro_mdom_1904, retro_mdom_35, retro_mdom_504, retro_mdom_589, retro_mdom_612, retro_mdom_639, retro_mdom_995,
Mustela putorius furo	ENSMPUG00000011734	6 retrocopies	retro_mputfur_137, retro_mputfur_187, retro_mputfur_370, retro_mputfur_467, retro_mputfur_816, retro_mputfur_970,
Mus musculus	ENSMUSG00000048758	3 retrocopies	retro_mmus_203, retro_mmus_231, retro_mmus_86,
Otolemur garnettii	ENSOGAG00000013766	2 retrocopies	retro_ogar_290, retro_ogar_31,
Ochotona princeps	ENSOPRG00000008821	10 retrocopies	retro_opri_1166, retro_opri_277, retro_opri_373, retro_opri_535, retro_opri_607, retro_opri_69, retro_opri_700, retro_opri_877, retro_opri_983, retro_opri_99,
Procavia capensis	ENSPCAG00000009712	4 retrocopies	retro_pcap_100, retro_pcap_101, retro_pcap_44, retro_pcap_97,
Pongo abelii	ENSPPYG00000013818	21 retrocopies	retro_pabe_1062, retro_pabe_1162, retro_pabe_1306, retro_pabe_1503, retro_pabe_1714, retro_pabe_1882, retro_pabe_2125, retro_pabe_2131, retro_pabe_2398, retro_pabe_2718, retro_pabe_2952, retro_pabe_3254, retro_pabe_3284, retro_pabe_3504, retro_pabe_3525, retro_pabe_404 , retro_pabe_459, retro_pabe_491, retro_pabe_673, retro_pabe_687, retro_pabe_911,
Rattus norvegicus	ENSRNOG00000011138	15 retrocopies	retro_rnor_1045, retro_rnor_1158, retro_rnor_1161, retro_rnor_1422, retro_rnor_1702, retro_rnor_184, retro_rnor_1951, retro_rnor_2207, retro_rnor_2222, retro_rnor_2356, retro_rnor_2561, retro_rnor_338, retro_rnor_397, retro_rnor_63, retro_rnor_928,
Sorex araneus	ENSSARG00000013572	8 retrocopies	retro_sara_108, retro_sara_309, retro_sara_329, retro_sara_347, retro_sara_400, retro_sara_53, retro_sara_637, retro_sara_669,
Sarcophilus harrisii	ENSSHAG00000006854	2 retrocopies	retro_shar_355, retro_shar_444,
Sus scrofa	ENSSSCG00000027573	7 retrocopies	retro_sscr_179, retro_sscr_182, retro_sscr_205, retro_sscr_206, retro_sscr_207, retro_sscr_208, retro_sscr_720,
Ictidomys tridecemlineatus	ENSSTOG00000020488	14 retrocopies	retro_itri_1345, retro_itri_1433, retro_itri_1482, retro_itri_1586, retro_itri_1664, retro_itri_1667, retro_itri_194, retro_itri_482, retro_itri_520, retro_itri_592, retro_itri_622, retro_itri_874, retro_itri_934, retro_itri_942,
Tursiops truncatus	ENSTTRG00000003514	5 retrocopies	retro_ttru_1933, retro_ttru_213, retro_ttru_409, retro_ttru_449, retro_ttru_985,
Vicugna pacos	ENSVPAG00000001282	29 retrocopies	retro_vpac_102, retro_vpac_110, retro_vpac_120, retro_vpac_148, retro_vpac_155, retro_vpac_176, retro_vpac_188, retro_vpac_199, retro_vpac_243, retro_vpac_264, retro_vpac_28, retro_vpac_302, retro_vpac_305, retro_vpac_317, retro_vpac_325, retro_vpac_40, retro_vpac_401, retro_vpac_41, retro_vpac_416, retro_vpac_453, retro_vpac_462, retro_vpac_481, retro_vpac_547, retro_vpac_575, retro_vpac_58, retro_vpac_60, retro_vpac_602, retro_vpac_636, retro_vpac_98,