RetrogeneDB ID: retro_pabe_228

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:25958416..25958688(+)
• Located in intron of: ENSPPYG00000000188

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000000326
• Aliases: None
• Description: None

Sequence

>retro_pabe_228
ATGGTGTACCGTGGTCAGGGCCAGAAAGTGCAGAAGGCTATGATGGAGCCCATCAACCTCATCTTCAGATTCTTACAAAA
TAGATCCCAGATTCATGTATGGCTCTATAAGCAGAGAATATGTGGATAGAAGGCTGTATCATTGGTTTTGATGAGTATAT
GAACCTTGTATTAGTTGATGCAGAAGAGATTTATTCTAAAACAAAGTTAAAACAACTTGGTTGGATCATGCTAAAAGGAG
ATAATATTACTTGGGTACATAGTGTCTCCAAC

Alignment

ORF - retro_pabe_228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQ-VNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK
          M.YRGQGQKVQK.M..PINLIFR.LQNRS.I.VWLY.Q..NM.IEGCIIGFDEYMNLVL.DAEEI.SKTK
Retrocopy MVYRGQGQKVQKAMMEPINLIFRFLQNRSQIHVWLYKQ<ENMWIEGCIIGFDEYMNLVLVDAEEIYSKTK

Parental  SRKQLGRIMLKGDNITLLQSVSN
          ..KQLG.IMLKGDNIT...SVSN
Retrocopy -LKQLGWIMLKGDNITWVHSVSN

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	4.64 RPM
SRP007412_cerebellum	0.00 RPM	6.69 RPM
SRP007412_heart	0.00 RPM	6.11 RPM
SRP007412_kidney	0.00 RPM	7.96 RPM
SRP007412_liver	0.00 RPM	6.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_228 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_228 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_516
Pan troglodytes	retro_ptro_385
Macaca mulatta	retro_mmul_427

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 188 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000882	8 retrocopies	retro_amel_1112, retro_amel_1206, retro_amel_1211, retro_amel_1293, retro_amel_1517, retro_amel_1530, retro_amel_185, retro_amel_412,
Choloepus hoffmanni	ENSCHOG00000009158	6 retrocopies	retro_chof_139, retro_chof_1870, retro_chof_1897, retro_chof_1981, retro_chof_2652, retro_chof_450,
Callithrix jacchus	ENSCJAG00000006735	1 retrocopy	retro_cjac_3163,
Dasypus novemcinctus	ENSDNOG00000004490	24 retrocopies	retro_dnov_1009, retro_dnov_1141, retro_dnov_122, retro_dnov_1223, retro_dnov_1312, retro_dnov_1314, retro_dnov_1362, retro_dnov_1438, retro_dnov_163, retro_dnov_191, retro_dnov_2398, retro_dnov_2671, retro_dnov_360, retro_dnov_414, retro_dnov_513, retro_dnov_579, retro_dnov_796, retro_dnov_828, retro_dnov_898, retro_dnov_900, retro_dnov_902, retro_dnov_93, retro_dnov_967, retro_dnov_983,
Erinaceus europaeus	ENSEEUG00000006187	6 retrocopies	retro_eeur_339, retro_eeur_497, retro_eeur_579, retro_eeur_613, retro_eeur_85, retro_eeur_92,
Echinops telfairi	ENSETEG00000014015	24 retrocopies	retro_etel_1136, retro_etel_1244, retro_etel_138, retro_etel_1443, retro_etel_1530, retro_etel_1636, retro_etel_1739, retro_etel_1781, retro_etel_1947, retro_etel_2143, retro_etel_234, retro_etel_258, retro_etel_310, retro_etel_377, retro_etel_466, retro_etel_546, retro_etel_56, retro_etel_579, retro_etel_581, retro_etel_582, retro_etel_76, retro_etel_776, retro_etel_799, retro_etel_80,
Felis catus	ENSFCAG00000000873	2 retrocopies	retro_fcat_1836, retro_fcat_554,
Homo sapiens	ENSG00000182004	10 retrocopies	retro_hsap_130, retro_hsap_1668, retro_hsap_2022, retro_hsap_2073, retro_hsap_2287, retro_hsap_3262, retro_hsap_4228, retro_hsap_4660, retro_hsap_516, retro_hsap_576,
Gorilla gorilla	ENSGGOG00000000755	7 retrocopies	retro_ggor_1462, retro_ggor_1626, retro_ggor_1700, retro_ggor_2221, retro_ggor_228, retro_ggor_2892, retro_ggor_91,
Loxodonta africana	ENSLAFG00000009349	3 retrocopies	retro_lafr_796, retro_lafr_814, retro_lafr_873,
Macropus eugenii	ENSMEUG00000015262	1 retrocopy	retro_meug_378,
Microcebus murinus	ENSMICG00000015537	3 retrocopies	retro_mmur_1406, retro_mmur_453, retro_mmur_58,
Myotis lucifugus	ENSMLUG00000013244	8 retrocopies	retro_mluc_1639, retro_mluc_1650, retro_mluc_1994, retro_mluc_2045, retro_mluc_2088, retro_mluc_2326, retro_mluc_85, retro_mluc_919,
Macaca mulatta	ENSMMUG00000031372	8 retrocopies	retro_mmul_1039, retro_mmul_1258, retro_mmul_1576, retro_mmul_1790, retro_mmul_1820, retro_mmul_2054, retro_mmul_2480, retro_mmul_427,
Monodelphis domestica	ENSMODG00000028394	3 retrocopies	retro_mdom_1164, retro_mdom_1790, retro_mdom_1865,
Mustela putorius furo	ENSMPUG00000011642	7 retrocopies	retro_mputfur_1078, retro_mputfur_1527, retro_mputfur_1634, retro_mputfur_53, retro_mputfur_638, retro_mputfur_729, retro_mputfur_949,
Mus musculus	ENSMUSG00000090553	10 retrocopies	retro_mmus_1527, retro_mmus_1597, retro_mmus_1704, retro_mmus_2090, retro_mmus_2788, retro_mmus_2953, retro_mmus_296, retro_mmus_3001, retro_mmus_3682, retro_mmus_898,
Otolemur garnettii	ENSOGAG00000004309	12 retrocopies	retro_ogar_2249, retro_ogar_2543, retro_ogar_2619, retro_ogar_2917, retro_ogar_3031, retro_ogar_3279, retro_ogar_748, retro_ogar_749, retro_ogar_750, retro_ogar_773, retro_ogar_774, retro_ogar_947,
Ochotona princeps	ENSOPRG00000015415	11 retrocopies	retro_opri_120, retro_opri_1215, retro_opri_314, retro_opri_359, retro_opri_450, retro_opri_453, retro_opri_580, retro_opri_601, retro_opri_613, retro_opri_786, retro_opri_856,
Pongo abelii	ENSPPYG00000000326	8 retrocopies	retro_pabe_1375, retro_pabe_20, retro_pabe_2023, retro_pabe_228 , retro_pabe_3015, retro_pabe_3620, retro_pabe_56, retro_pabe_610,
Pan troglodytes	ENSPTRG00000030224	11 retrocopies	retro_ptro_1131, retro_ptro_134, retro_ptro_1345, retro_ptro_1346, retro_ptro_1526, retro_ptro_1620, retro_ptro_2206, retro_ptro_2872, retro_ptro_3096, retro_ptro_385, retro_ptro_426,
Sorex araneus	ENSSARG00000003311	9 retrocopies	retro_sara_171, retro_sara_173, retro_sara_183, retro_sara_214, retro_sara_219, retro_sara_37, retro_sara_664, retro_sara_697, retro_sara_750,
Sarcophilus harrisii	ENSSHAG00000002978	1 retrocopy	retro_shar_357,
Sus scrofa	ENSSSCG00000023562	3 retrocopies	retro_sscr_1159, retro_sscr_172, retro_sscr_606,
Vicugna pacos	ENSVPAG00000011162	2 retrocopies	retro_vpac_469, retro_vpac_477,