RetrogeneDB ID: retro_pabe_3405

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:45832543..45833014(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000025842
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000019622
• Aliases: None
• Description: None

Sequence

>retro_pabe_3405
GAGATCAAAGTCGTATATCTGAGGTGCACCAGAGGTGAAGTCGGTGCCACTTCTGCCCTGGCCCCCAAGATCGGTCCCCT
GGGTCTGTCTCCAAAAAAGGTTGGTGATGACATTGCCGAGGCAACGGGTGACTGGAAGGGCCTGAGGATTACAGTGAAAC
TGACCATTCAGAACAGACAGGCCCAGATTGAGGTGGTGCCTTCTGCCTCTGCCCTGATGATCAAAGCCCTCAAGGAACCA
CCAAGAGACAGAAAGAAACAGAAAAACATTAAACACAGTGGGAATATCACTTTTGATGAGATCGTCAACATTGCTCGACA
GATGCGGCACCGATCCTTAGCCAGAGAACTCTCTGGAACCATTAAAGAGATCCTGGGGACTGCCCAGTCTGTGGGCTGTA
ATGTTGATGGCCGCCACCCTCATGACATCATAGATGACATCAATAGTGGTGCTGTGGAATGCCCAGCCAGT

Alignment

ORF - retro_pabe_3405 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.09 %
• Parental protein coverage: 68.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQIEVVPSAS
          EIKVVYLRCT.GEVGATSALAPKIGPLGLSPKKVGDDIA.ATGDWKGLRITVKLTIQNRQAQIEVVPSAS
Retrocopy EIKVVYLRCTRGEVGATSALAPKIGPLGLSPKKVGDDIAEATGDWKGLRITVKLTIQNRQAQIEVVPSAS

Parental  ALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHP
          AL.IKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHP
Retrocopy ALMIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHP

Parental  HDIIDDINSGAVECPAS
          HDIIDDINSGAVECPAS
Retrocopy HDIIDDINSGAVECPAS

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	80.56 RPM
SRP007412_cerebellum	0.00 RPM	46.21 RPM
SRP007412_heart	0.00 RPM	94.65 RPM
SRP007412_kidney	0.03 RPM	193.41 RPM
SRP007412_liver	0.03 RPM	195.27 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3405 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3405 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 369 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006963	3 retrocopies	retro_btau_102, retro_btau_2, retro_btau_5,
Callithrix jacchus	ENSCJAG00000018082	1 retrocopy	retro_cjac_221,
Homo sapiens	ENSG00000197958	41 retrocopies	retro_hsap_1064, retro_hsap_117, retro_hsap_1210, retro_hsap_127, retro_hsap_1311, retro_hsap_1359, retro_hsap_137, retro_hsap_1401, retro_hsap_1592, retro_hsap_1644, retro_hsap_1790, retro_hsap_1850, retro_hsap_1880, retro_hsap_1895, retro_hsap_2005, retro_hsap_2031, retro_hsap_2099, retro_hsap_2123, retro_hsap_2202, retro_hsap_2311, retro_hsap_2381, retro_hsap_2428, retro_hsap_2436, retro_hsap_2456, retro_hsap_2642, retro_hsap_3388, retro_hsap_3405, retro_hsap_3458, retro_hsap_3544, retro_hsap_3578, retro_hsap_3709, retro_hsap_4107, retro_hsap_4121, retro_hsap_4746, retro_hsap_584, retro_hsap_643, retro_hsap_705, retro_hsap_719, retro_hsap_768, retro_hsap_868, retro_hsap_983,
Gorilla gorilla	ENSGGOG00000000648	34 retrocopies	retro_ggor_1024, retro_ggor_1059, retro_ggor_1086, retro_ggor_1207, retro_ggor_1242, retro_ggor_1377, retro_ggor_1389, retro_ggor_1449, retro_ggor_1511, retro_ggor_1516, retro_ggor_1530, retro_ggor_1645, retro_ggor_1740, retro_ggor_1753, retro_ggor_1806, retro_ggor_1845, retro_ggor_2158, retro_ggor_221, retro_ggor_2232, retro_ggor_2293, retro_ggor_2304, retro_ggor_232, retro_ggor_2334, retro_ggor_2394, retro_ggor_2414, retro_ggor_2506, retro_ggor_262, retro_ggor_2758, retro_ggor_2768, retro_ggor_2949, retro_ggor_541, retro_ggor_600, retro_ggor_637, retro_ggor_942,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Macaca mulatta	ENSMMUG00000000422	2 retrocopies	retro_mmul_1823, retro_mmul_53,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Mus musculus	ENSMUSG00000038900	1 retrocopy	retro_mmus_28,
Oryctolagus cuniculus	ENSOCUG00000004902	9 retrocopies	retro_ocun_1246, retro_ocun_1632, retro_ocun_1895, retro_ocun_318, retro_ocun_329, retro_ocun_520, retro_ocun_556, retro_ocun_677, retro_ocun_880,
Otolemur garnettii	ENSOGAG00000000597	120 retrocopies	retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Ochotona princeps	ENSOPRG00000011078	21 retrocopies	retro_opri_100, retro_opri_1018, retro_opri_1066, retro_opri_1110, retro_opri_1210, retro_opri_1217, retro_opri_221, retro_opri_265, retro_opri_336, retro_opri_353, retro_opri_418, retro_opri_461, retro_opri_479, retro_opri_576, retro_opri_638, retro_opri_648, retro_opri_658, retro_opri_672, retro_opri_835, retro_opri_905, retro_opri_986,
Pongo abelii	ENSPPYG00000019622	44 retrocopies	retro_pabe_1009, retro_pabe_1084, retro_pabe_1095, retro_pabe_1127, retro_pabe_1159, retro_pabe_1223, retro_pabe_1246, retro_pabe_1309, retro_pabe_1361, retro_pabe_1471, retro_pabe_1509, retro_pabe_1577, retro_pabe_1659, retro_pabe_1660, retro_pabe_1736, retro_pabe_1794, retro_pabe_1806, retro_pabe_1820, retro_pabe_1969, retro_pabe_1982, retro_pabe_2000, retro_pabe_2149, retro_pabe_2328, retro_pabe_2531, retro_pabe_2802, retro_pabe_2859, retro_pabe_2928, retro_pabe_2947, retro_pabe_3002, retro_pabe_3146, retro_pabe_3185, retro_pabe_3276, retro_pabe_3363, retro_pabe_3405 , retro_pabe_3482, retro_pabe_3693, retro_pabe_488, retro_pabe_521, retro_pabe_604, retro_pabe_620, retro_pabe_757, retro_pabe_815, retro_pabe_831, retro_pabe_904,
Pan troglodytes	ENSPTRG00000022808	1 retrocopy	retro_ptro_21,
Pteropus vampyrus	ENSPVAG00000000925	15 retrocopies	retro_pvam_100, retro_pvam_1026, retro_pvam_1193, retro_pvam_209, retro_pvam_239, retro_pvam_483, retro_pvam_572, retro_pvam_590, retro_pvam_617, retro_pvam_630, retro_pvam_687, retro_pvam_747, retro_pvam_787, retro_pvam_846, retro_pvam_888,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Sarcophilus harrisii	ENSSHAG00000017864	8 retrocopies	retro_shar_140, retro_shar_266, retro_shar_284, retro_shar_335, retro_shar_346, retro_shar_453, retro_shar_508, retro_shar_646,
Sus scrofa	ENSSSCG00000005612	14 retrocopies	retro_sscr_1111, retro_sscr_127, retro_sscr_189, retro_sscr_28, retro_sscr_439, retro_sscr_526, retro_sscr_551, retro_sscr_71, retro_sscr_715, retro_sscr_772, retro_sscr_773, retro_sscr_828, retro_sscr_832, retro_sscr_911,
Vicugna pacos	ENSVPAG00000005123	27 retrocopies	retro_vpac_158, retro_vpac_181, retro_vpac_189, retro_vpac_191, retro_vpac_194, retro_vpac_236, retro_vpac_268, retro_vpac_276, retro_vpac_291, retro_vpac_306, retro_vpac_323, retro_vpac_36, retro_vpac_37, retro_vpac_377, retro_vpac_413, retro_vpac_43, retro_vpac_432, retro_vpac_465, retro_vpac_482, retro_vpac_494, retro_vpac_506, retro_vpac_55, retro_vpac_569, retro_vpac_615, retro_vpac_80, retro_vpac_83, retro_vpac_90,