RetrogeneDB ID: retro_pabe_2549

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:114220946..114221692(-)
• Located in intron of: ENSPPYG00000029772

Retrocopy information

• Ensembl ID: ENSPPYG00000014991
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000019659
• Aliases: None
• Description: None

Sequence

>retro_pabe_2549
ATGGCCCCCAAATGCCAGTCTTCCCTCCTGTCTCAAAAGAAGACACCAAGACCACCTCCTGTTCTGAGACCAGAGGAGAC
TTCGGCCTCTGTAGGCTTGCCAAAGAAGGGCGAAAAAGAACAGCAAGAAGCAATTGAACACATTGATGAAATACAAAATG
AAATAGACAGACTTAATGAACAAGACAGTGAGGAGATTTTGAAAGTAGAACAGAAATATAACAAACTCCGCCAACCATTT
TTTCAGAAGAGGTCAGAATTGATCTCCAAAATCCTAAATTTGGGGGTAACAACATTTGGCAATCATTTACAAGTGTCTGC
ACTGCTTGGGAAGGAAAACGAAGAGGCATTGCATTATTTGACCAGAGTTGAAGTGACAGAATTTGAAGATATTAAATCAG
GTTACAGAGTAGATTTTTATTTTGATGAAAATCCTTACTTTGAAAAAAAGTTCTCTCCAAAGAATTTCATCTGAATGAGA
GTATTAATCCATCTTCAAAATCCACTGAAATCAAATGGAAATCTGGAAAGGATGTGATGAAACGTTTAAGTCAAATGCAG
AATAAAGCCAGCAGGAAGAGGCAGCATGAGGCACCAGAGAGCTTCTTGACCTGGTTTACTGACCATTCTGATGCAGGGGC
CGATGACTTAGGAGAGGACATCAAAGATGATATTTGGCCAAACCCATTACAGTACTATTTGGTTCCCGATATGGATGATG
AAGAAGGAGAAGATGATAATGAGGAG

Alignment

ORF - retro_pabe_2549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.2 %
• Parental protein coverage: 85.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPKRQSPLPPQKKKPRPPPALGPEETLASAGLPKKGEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVE
          MAPK.QS.L..QKK.PRPPP.L.PEET.AS.GLPKKGEKEQQEAIEHIDE.QNEIDRLNEQ.SEEILKVE
Retrocopy MAPKCQSSLLSQKKTPRPPPVLRPEETSASVGLPKKGEKEQQEAIEHIDEIQNEIDRLNEQDSEEILKVE

Parental  QKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFY
          QKYNKLRQPFFQKRSELI.KI.N..VTTF.NH.QVSALLG.E.EEALHYLTRVEVTEFEDIKSGYR.DFY
Retrocopy QKYNKLRQPFFQKRSELISKILNLGVTTFGNHLQVSALLGKENEEALHYLTRVEVTEFEDIKSGYRVDFY

Parental  FDENPYFE-NKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDH
          FDENPYFE..KVLSKEFHLNES..PSSKSTEIKWKSGKD..KR.SQ.QNKASRKRQHE.PESF.TWFTDH
Retrocopy FDENPYFE<KKVLSKEFHLNESINPSSKSTEIKWKSGKDVMKRLSQMQNKASRKRQHEAPESFLTWFTDH

Parental  SDAGADELGEVIKDDIWPNPLQYYLVPDMDDEEGEGEEDD
          SDAGAD.LGE.IKDDIWPNPLQYYLVPDMDDEEGE.....
Retrocopy SDAGADDLGEDIKDDIWPNPLQYYLVPDMDDEEGEDDNEE

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	83.16 RPM
SRP007412_cerebellum	0.12 RPM	86.34 RPM
SRP007412_heart	0.06 RPM	51.00 RPM
SRP007412_kidney	0.00 RPM	84.13 RPM
SRP007412_liver	0.03 RPM	59.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2549 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2549 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3075
Pan troglodytes	retro_ptro_2073

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 194 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris	ENSCAFG00000032728	2 retrocopies	retro_cfam_47, retro_cfam_83,
Dasypus novemcinctus	ENSDNOG00000002802	3 retrocopies	retro_dnov_160, retro_dnov_1830, retro_dnov_464,
Equus caballus	ENSECAG00000009117	4 retrocopies	retro_ecab_358, retro_ecab_417, retro_ecab_505, retro_ecab_675,
Erinaceus europaeus	ENSEEUG00000006238	11 retrocopies	retro_eeur_152, retro_eeur_166, retro_eeur_173, retro_eeur_210, retro_eeur_260, retro_eeur_287, retro_eeur_452, retro_eeur_659, retro_eeur_696, retro_eeur_700, retro_eeur_701,
Echinops telfairi	ENSETEG00000016746	15 retrocopies	retro_etel_1039, retro_etel_109, retro_etel_1123, retro_etel_1372, retro_etel_1649, retro_etel_1790, retro_etel_1872, retro_etel_1880, retro_etel_1930, retro_etel_1937, retro_etel_2110, retro_etel_2159, retro_etel_835, retro_etel_920, retro_etel_939,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Homo sapiens	ENSG00000119335	14 retrocopies	retro_hsap_1336, retro_hsap_1389, retro_hsap_1847, retro_hsap_241, retro_hsap_269, retro_hsap_2719, retro_hsap_2721, retro_hsap_3075, retro_hsap_3088, retro_hsap_3326, retro_hsap_3358, retro_hsap_420, retro_hsap_4722, retro_hsap_806,
Microcebus murinus	ENSMICG00000017643	2 retrocopies	retro_mmur_1398, retro_mmur_775,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Macaca mulatta	ENSMMUG00000008532	11 retrocopies	retro_mmul_1133, retro_mmul_1261, retro_mmul_1534, retro_mmul_2096, retro_mmul_2175, retro_mmul_2241, retro_mmul_2262, retro_mmul_2614, retro_mmul_362, retro_mmul_419, retro_mmul_569,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Mus musculus	ENSMUSG00000054766	17 retrocopies	retro_mmus_1366, retro_mmus_1435, retro_mmus_1671, retro_mmus_1743, retro_mmus_2329, retro_mmus_2448, retro_mmus_2484, retro_mmus_2664, retro_mmus_2665, retro_mmus_3015, retro_mmus_3290, retro_mmus_345, retro_mmus_3513, retro_mmus_517, retro_mmus_887, retro_mmus_929, retro_mmus_967,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus	ENSOCUG00000007501	12 retrocopies	retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549 , retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Pan troglodytes	ENSPTRG00000021436	16 retrocopies	retro_ptro_1232, retro_ptro_1836, retro_ptro_1838, retro_ptro_2073, retro_ptro_2085, retro_ptro_209, retro_ptro_2151, retro_ptro_2152, retro_ptro_225, retro_ptro_2283, retro_ptro_2965, retro_ptro_3140, retro_ptro_321, retro_ptro_561, retro_ptro_913, retro_ptro_953,
Pteropus vampyrus	ENSPVAG00000003437	2 retrocopies	retro_pvam_1198, retro_pvam_886,
Ictidomys tridecemlineatus	ENSSTOG00000010546	6 retrocopies	retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,
Tursiops truncatus	ENSTTRG00000011605	7 retrocopies	retro_ttru_1433, retro_ttru_1600, retro_ttru_181, retro_ttru_1901, retro_ttru_537, retro_ttru_919, retro_ttru_931,