RetrogeneDB ID: retro_pabe_1816

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:27232828..27233408(-)
• Located in intron of: ENSPPYG00000010859

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSPPYG00000017336
• Aliases: None
• Description: Actin, cytoplasmic 1 Actin, cytoplasmic 1, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:Q5R6G0]

Sequence

>retro_pabe_1816
GGCCGGCCAGGACCTGACCACCTCATGAAGATTCTCACAGAATATGACTACAGCTTCCCTACCACGGCCAAGTGGGAGAT
CGTGCGTGACATCAAGGAGAGGCAGTGCTACGTTGCCCTGGACTTTGAGCAGGAGATGGCCACCACTACGTCATCCTTCT
CCCTGGAGAAAAGCTACAAACTACCTGACAGCCAGGTGATCACCATTGGCAACATGCAGTTCCAGTGTTTGGAGGCGTTG
TTCCAGCCCTTCTTTCTGGGTGTGGAATTTTGCAGCATCCATGTGGAATTTTGCAGCTCCATCATAAGGTGTGATGTGGA
CATCCACAAGGACCTGTATGCCAACACGATGCTGGCCAGTGGCACCACCATGTACCCAAGCATCTCCAGCAGGATGCAGA
AAGAGATCACTGCCCTGGTGCCAGCACAAGTAAGATCAAGATCATCGTGCTCCCAGAGCACAAGTACTCCGTGTGGATCA
GCAGCTCCATCCTGGCCTCGTTGTCCACTTTCCAGCAGATGTGGATTAGCAAGCAGGAATATGACAAGTCGGGCCCCTCC
ATGTCCACCGCAAATGCTTC

Alignment

ORF - retro_pabe_1816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 51.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIG
          GR...D.LMKILTE..YSF.TTA..EIVRDIKE..CYVALDFEQEMAT..SS.SLEKSY.LPD.QVITIG
Retrocopy GRPGPDHLMKILTEYDYSFPTTAKWEIVRDIKERQCYVALDFEQEMATTTSSFSLEKSYKLPDSQVITIG

Parental  NERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALA
          N..F.C.EALFQP.FL.................CDVDI.KDLYANT.L..GTTMYP.I..RMQKEITAL.
Retrocopy NMQFQCLEALFQPFFLXXXXXXXXXXXXXXXIRCDVDIHKDLYANTMLASGTTMYPSISSRMQKEITALV

Parental  P-STMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSI-VHRKCF
          P.ST.KIKII..PE.KYSVWI..SILASLSTFQQMWISKQEYD.SGPS..VHRKCF
Retrocopy P<STSKIKIIVLPEHKYSVWISSSILASLSTFQQMWISKQEYDKSGPSM<VHRKCF

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	1655.73 RPM
SRP007412_cerebellum	0.00 RPM	578.33 RPM
SRP007412_heart	0.03 RPM	386.86 RPM
SRP007412_kidney	0.10 RPM	1247.35 RPM
SRP007412_liver	0.15 RPM	1654.82 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1816 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1816 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2405
Gorilla gorilla	retro_ggor_1495

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Pongo abelii	ENSPPYG00000002605	1 retrocopy	retro_pabe_1930,
Pongo abelii	ENSPPYG00000006318	1 retrocopy	retro_pabe_1317,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816 , retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,