RetrogeneDB ID: retro_pabe_3304

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:18228418..18228762(-)
• Located in intron of: ENSPPYG00000018396

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL35
• Ensembl ID: ENSPPYG00000019603
• Aliases: None
• Description: ribosomal protein L35 [Source:HGNC Symbol;Acc:10344]

Sequence

>retro_pabe_3304
GTAGCCAAGATTAAGGCTCAGGATCTTTGAGGCAAGAAGGAAGAGGAGCTGCTAAGACAGCTGGACAACCTGAAGGTAGA
CCTGTCCCAGATGTATTTCGCCAAAGTGACAGGTGCCCGACATTCCAGTTCTCTTAGATTGTAGTCATTTCCAAATCTGT
TGCCTGTGTTCTCACCGTCATTAGCCAAACTCAGAAAACAAACCTCAGGAAGTTCTACAAGAGCAAGAAATACTAGCCCC
CAGATCTGTGGCCCAAGAATGCTTGTATCATGTGCCACTGGCTGAACAAGCATAGGGAGAACCTGAAGATCAAGAAGCAG
CAGCAGCAGGAACAGGCTGTACCA

Alignment

ORF - retro_pabe_3304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.79 %
• Parental protein coverage: 93.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAAS-KLSKIRVVRKSIARVLTVINQTQKENL
          .AKIKA.DL.GKK.EELL.QLD.LKV.LSQ...AKVTG...S...S.I.V..KS.A.VLTVI.QTQK.NL
Retrocopy VAKIKAQDL*GKKEEELLRQLDNLKVDLSQMYFAKVTGARHS<QFS*IVVISKSVACVLTVISQTQKTNL

Parental  RKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYP
          RKFYK.KKY.P.DL.PK....M...LNKH.ENLK.KKQQ..E...P
Retrocopy RKFYKSKKY*PPDLWPKNACIMCHWLNKHRENLKIKKQQQQEQAVP

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	88.69 RPM
SRP007412_cerebellum	0.12 RPM	57.76 RPM
SRP007412_heart	0.12 RPM	65.17 RPM
SRP007412_kidney	0.00 RPM	170.74 RPM
SRP007412_liver	0.12 RPM	141.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3304 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3304 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 139 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016537	12 retrocopies	retro_amel_1010, retro_amel_1180, retro_amel_1341, retro_amel_1686, retro_amel_1746, retro_amel_1844, retro_amel_1887, retro_amel_351, retro_amel_584, retro_amel_819, retro_amel_893, retro_amel_94,
Bos taurus	ENSBTAG00000003205	3 retrocopies	retro_btau_1060, retro_btau_1340, retro_btau_185,
Canis familiaris	ENSCAFG00000020212	7 retrocopies	retro_cfam_1566, retro_cfam_1635, retro_cfam_2180, retro_cfam_294, retro_cfam_529, retro_cfam_738, retro_cfam_995,
Callithrix jacchus	ENSCJAG00000006724	5 retrocopies	retro_cjac_1074, retro_cjac_1308, retro_cjac_1377, retro_cjac_2458, retro_cjac_387,
Cavia porcellus	ENSCPOG00000022811	1 retrocopy	retro_cpor_414,
Equus caballus	ENSECAG00000009389	3 retrocopies	retro_ecab_1083, retro_ecab_115, retro_ecab_813,
Erinaceus europaeus	ENSEEUG00000012696	8 retrocopies	retro_eeur_144, retro_eeur_217, retro_eeur_225, retro_eeur_251, retro_eeur_319, retro_eeur_487, retro_eeur_533, retro_eeur_56,
Echinops telfairi	ENSETEG00000000876	10 retrocopies	retro_etel_1013, retro_etel_1267, retro_etel_1383, retro_etel_1556, retro_etel_1848, retro_etel_1931, retro_etel_303, retro_etel_637, retro_etel_747, retro_etel_942,
Felis catus	ENSFCAG00000030388	5 retrocopies	retro_fcat_1129, retro_fcat_1790, retro_fcat_1954, retro_fcat_397, retro_fcat_782,
Homo sapiens	ENSG00000136942	6 retrocopies	retro_hsap_1233, retro_hsap_326, retro_hsap_3579, retro_hsap_3832, retro_hsap_3867, retro_hsap_4026,
Gorilla gorilla	ENSGGOG00000004111	3 retrocopies	retro_ggor_2581, retro_ggor_351, retro_ggor_966,
Loxodonta africana	ENSLAFG00000010031	3 retrocopies	retro_lafr_128, retro_lafr_300, retro_lafr_642,
Microcebus murinus	ENSMICG00000002922	2 retrocopies	retro_mmur_1502, retro_mmur_215,
Myotis lucifugus	ENSMLUG00000029323	3 retrocopies	retro_mluc_1495, retro_mluc_2392, retro_mluc_969,
Macaca mulatta	ENSMMUG00000005260	5 retrocopies	retro_mmul_1304, retro_mmul_156, retro_mmul_1623, retro_mmul_1912, retro_mmul_265,
Monodelphis domestica	ENSMODG00000019753	1 retrocopy	retro_mdom_1039,
Mustela putorius furo	ENSMPUG00000013950	5 retrocopies	retro_mputfur_1136, retro_mputfur_1348, retro_mputfur_1478, retro_mputfur_1484, retro_mputfur_425,
Mus musculus	ENSMUSG00000062997	1 retrocopy	retro_mmus_236,
Nomascus leucogenys	ENSNLEG00000017303	7 retrocopies	retro_nleu_1153, retro_nleu_1770, retro_nleu_1850, retro_nleu_1921, retro_nleu_2104, retro_nleu_2836, retro_nleu_953,
Ornithorhynchus anatinus	ENSOANG00000011612	1 retrocopy	retro_oana_56,
Oryctolagus cuniculus	ENSOCUG00000002996	4 retrocopies	retro_ocun_200, retro_ocun_238, retro_ocun_451, retro_ocun_791,
Otolemur garnettii	ENSOGAG00000008513	7 retrocopies	retro_ogar_1265, retro_ogar_1271, retro_ogar_1828, retro_ogar_2005, retro_ogar_2253, retro_ogar_2610, retro_ogar_2903,
Ochotona princeps	ENSOPRG00000000406	9 retrocopies	retro_opri_1077, retro_opri_1134, retro_opri_244, retro_opri_273, retro_opri_339, retro_opri_473, retro_opri_565, retro_opri_628, retro_opri_650,
Pongo abelii	ENSPPYG00000019603	7 retrocopies	retro_pabe_1026, retro_pabe_165, retro_pabe_1718, retro_pabe_2948, retro_pabe_3064, retro_pabe_3303, retro_pabe_3304 ,
Rattus norvegicus	ENSRNOG00000014272	14 retrocopies	retro_rnor_1254, retro_rnor_126, retro_rnor_147, retro_rnor_1473, retro_rnor_1509, retro_rnor_1768, retro_rnor_1957, retro_rnor_205, retro_rnor_2183, retro_rnor_233, retro_rnor_2618, retro_rnor_2681, retro_rnor_2719, retro_rnor_451,
Sarcophilus harrisii	ENSSHAG00000004756	1 retrocopy	retro_shar_775,
Sus scrofa	ENSSSCG00000005595	5 retrocopies	retro_sscr_1168, retro_sscr_214, retro_sscr_553, retro_sscr_679, retro_sscr_905,
Ictidomys tridecemlineatus	ENSSTOG00000007901	1 retrocopy	retro_itri_1735,