RetrogeneDB ID: retro_pabe_562

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:116206146..116206776(+)
• Located in intron of: ENSPPYG00000002685

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000001152
• Aliases: None
• Description: None

Sequence

>retro_pabe_562
CGCTCACATAACACAGAGAATGTCTGTCACATTGCTTATGCCTGTATGGAAGGGGATATGATAGTTTGTATACCTTATGC
TCATGAGCTACCAAAACATGGTGTGAAGGTTGGCCTGACAAATTACGCTGCGGCACATTGTCCTGGCCTGCTGATGGCCT
GCAGGCTTCTCAATAGGTCTGGCATGGGCAAGTTCTATGAAGGCCAAGTGGAGGTGACTGGTGATGAATACAATGTAGAA
AGCACTTATGGTCAGCCTGGTGCCTTCACTTGCTATTTGGATGCAGGCCTTGCCAAAACTACCTCTGGCAATAAAGTCTT
GGGGGGCCTTGAAGGCAGCTGCAGATGGAGGCTTGTCTACTCCTCTTGGTACCCAGTGATTCCCTGGTTATGATTTTGAA
AACAAGGAATTTAATGCAGAAGTGCATTAAAAGCACATCATCGGTCAGAATGTCGTGGATTACACGCATTTCCTAACAGA
AGATGAAGATGCTTACAAAAAACAATTCTCTCAATACATAGAAAACAGCGTAACTCCAGGCATGGAGGAGGTGTAGAAGA
GGGTAACGCTGCTATGCAACAGAATACAGTCTATGGGAAGAAACCCAAGAAAGAAGTTTAAATAAAGAGA

Alignment

ORF - retro_pabe_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.9 %
• Parental protein coverage: 71.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQV
          R..N....C.IAYA..EGDMIVC..YAHELPK.GVKVGLTNYAAA.C.GLL.A.RLLNR.GM.K.YEGQV
Retrocopy RSHNTENVCHIAYACMEGDMIVCIPYAHELPKHGVKVGLTNYAAAHCPGLLMACRLLNRSGMGKFYEGQV

Parental  EVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKV-FGALKGAVDGGLSIPHSTKRFPGYDSESKEFNA
          EVTGDEYNVES..GQPGAFTCYLDAGLA.TT.GNKV..GALK.A.DGGLS.P..T..FPGYD.E.KEFNA
Retrocopy EVTGDEYNVESTYGQPGAFTCYLDAGLAKTTSGNKV>WGALKAAADGGLSTPLGTQ*FPGYDFENKEFNA

Parental  EVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKK-AHAAIRENPVYEKKPKKEV
          EVH.KHI.GQNV.DY...L..EDEDAYKKQFSQYI.NSVTP..MEE..K....AA...N.VY.KKPKKEV
Retrocopy EVH*KHIIGQNVVDYTHFL-TEDEDAYKKQFSQYIENSVTPG-MEEV*KR<GNAAMQQNTVYGKKPKKEV

Parental  KKKR
          ..KR
Retrocopy *IKR

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	0.17 RPM	43.02 RPM
SRP007412_cerebellum	0.24 RPM	43.29 RPM
SRP007412_heart	0.00 RPM	58.73 RPM
SRP007412_kidney	0.00 RPM	101.00 RPM
SRP007412_liver	0.06 RPM	85.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_562 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 166 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020150	4 retrocopies	retro_cfam_1505, retro_cfam_1696, retro_cfam_905, retro_cfam_906,
Erinaceus europaeus	ENSEEUG00000002852	1 retrocopy	retro_eeur_620,
Echinops telfairi	ENSETEG00000009889	8 retrocopies	retro_etel_1044, retro_etel_1089, retro_etel_1103, retro_etel_1264, retro_etel_2028, retro_etel_64, retro_etel_785, retro_etel_814,
Felis catus	ENSFCAG00000024680	5 retrocopies	retro_fcat_281, retro_fcat_304, retro_fcat_453, retro_fcat_458, retro_fcat_463,
Homo sapiens	ENSG00000122406	30 retrocopies	retro_hsap_1266, retro_hsap_138, retro_hsap_1469, retro_hsap_1539, retro_hsap_1588, retro_hsap_1767, retro_hsap_183, retro_hsap_1989, retro_hsap_2143, retro_hsap_2385, retro_hsap_2594, retro_hsap_2600, retro_hsap_2777, retro_hsap_2962, retro_hsap_3105, retro_hsap_3178, retro_hsap_3181, retro_hsap_3209, retro_hsap_3430, retro_hsap_3520, retro_hsap_3941, retro_hsap_4048, retro_hsap_4104, retro_hsap_486, retro_hsap_590, retro_hsap_632, retro_hsap_646, retro_hsap_742, retro_hsap_780, retro_hsap_827,
Gorilla gorilla	ENSGGOG00000002699	24 retrocopies	retro_ggor_1129, retro_ggor_1172, retro_ggor_1206, retro_ggor_1342, retro_ggor_1343, retro_ggor_1656, retro_ggor_1934, retro_ggor_2052, retro_ggor_2130, retro_ggor_2178, retro_ggor_2243, retro_ggor_2318, retro_ggor_233, retro_ggor_2380, retro_ggor_264, retro_ggor_2649, retro_ggor_2715, retro_ggor_2755, retro_ggor_457, retro_ggor_521, retro_ggor_553, retro_ggor_622, retro_ggor_647, retro_ggor_996,
Loxodonta africana	ENSLAFG00000011916	6 retrocopies	retro_lafr_1025, retro_lafr_1098, retro_lafr_302, retro_lafr_988, retro_lafr_989, retro_lafr_992,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus	ENSMLUG00000008956	1 retrocopy	retro_mluc_925,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Nomascus leucogenys	ENSNLEG00000010500	2 retrocopies	retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Otolemur garnettii	ENSOGAG00000013246	6 retrocopies	retro_ogar_1164, retro_ogar_134, retro_ogar_1627, retro_ogar_2374, retro_ogar_2633, retro_ogar_707,
Procavia capensis	ENSPCAG00000011865	2 retrocopies	retro_pcap_159, retro_pcap_201,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pongo abelii	ENSPPYG00000001152	32 retrocopies	retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562 , retro_pabe_572, retro_pabe_637, retro_pabe_740,
Pan troglodytes	ENSPTRG00000000963	30 retrocopies	retro_ptro_1038, retro_ptro_1068, retro_ptro_1184, retro_ptro_1326, retro_ptro_139, retro_ptro_1519, retro_ptro_1524, retro_ptro_1568, retro_ptro_169, retro_ptro_1744, retro_ptro_1878, retro_ptro_2005, retro_ptro_2241, retro_ptro_2262, retro_ptro_2264, retro_ptro_2329, retro_ptro_2391, retro_ptro_2674, retro_ptro_2742, retro_ptro_2785, retro_ptro_2941, retro_ptro_3027, retro_ptro_366, retro_ptro_433, retro_ptro_460, retro_ptro_470, retro_ptro_528, retro_ptro_577, retro_ptro_866, retro_ptro_997,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Tarsius syrichta	ENSTSYG00000014038	8 retrocopies	retro_tsyr_1462, retro_tsyr_1548, retro_tsyr_206, retro_tsyr_248, retro_tsyr_670, retro_tsyr_737, retro_tsyr_786, retro_tsyr_952,