RetrogeneDB ID: retro_pabe_3670

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:87354754..87355139(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D2
• Ensembl ID: ENSPPYG00000015844
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 2 [Source:HGNC Symbol;Acc:12475]

Sequence

>retro_pabe_3670
ATGTAACTGAAGCAGATTAATAAGGAATTTAGGGTTTTTGTCCTTGGCCCTCTAGCACAGTGTTCTGTTGGATGTGATAG
GTTTCATTGGCAGGCTACAATTATAGGACCTCATTACATCCTGTATCAAGGTGGGTGTGTTCTTCTTGACAGTTCATTTT
CATTCAGATTACCCCTTCAAACCACCTAAGGTTGCATTTATTACAAGAATTTACCAACCAAACATTTAAGTAATGAGACC
ATTTGTCTCAGTATTCTAAGATTACCGTGGTCTTCTGCTTTAACATTTTTAAAGTTATTTTTACATCAATTTGTTCACTG
TTATGTGATCCAAATCCAGAAACCTTCTAGTGCTAGAGATTGCAAGGACCTATAAAACAGACAAA

Alignment

ORF - retro_pabe_3670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.44 %
• Parental protein coverage: 89.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGG-VFFLTIHFPTDYPFKPPKVAF
          M.LK.I.KE.......P.AQCS...VG.D.FHWQATI.GP....YQGG.VFFLT.HF..DYPFKPPKVAF
Retrocopy M*LKQINKEFRVFVLGPLAQCS---VGCDRFHWQATIIGPHYILYQGG>VFFLTVHFHSDYPFKPPKVAF

Parental  TTRIYHPNI-NSNGSICLDILRSQWSPALT-ISKVLL-SICSLLCDPNPD-DPLVPEIARIYKTDR
          .TRIY.PNI..SN..ICL.ILR..WS.ALT.I.KV...SICSLLCDPNP....LV.EIAR.YKTD.
Retrocopy ITRIYQPNI<LSNETICLSILRLPWSSALT<IFKVIFTSICSLLCDPNPE<NLLVLEIARTYKTDK

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	23.00 RPM
SRP007412_cerebellum	0.00 RPM	17.27 RPM
SRP007412_heart	0.00 RPM	13.00 RPM
SRP007412_kidney	0.00 RPM	16.57 RPM
SRP007412_liver	0.00 RPM	11.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3670 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3670 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2515

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002183	1 retrocopy	retro_acar_182,
Ailuropoda melanoleuca	ENSAMEG00000011216	6 retrocopies	retro_amel_1295, retro_amel_1427, retro_amel_1648, retro_amel_1750, retro_amel_620, retro_amel_995,
Bos taurus	ENSBTAG00000004161	6 retrocopies	retro_btau_1421, retro_btau_1602, retro_btau_1739, retro_btau_1775, retro_btau_1851, retro_btau_1852,
Canis familiaris	ENSCAFG00000031041	5 retrocopies	retro_cfam_1191, retro_cfam_1439, retro_cfam_1602, retro_cfam_2034, retro_cfam_785,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Loxodonta africana	ENSLAFG00000006878	2 retrocopies	retro_lafr_288, retro_lafr_290,
Macaca mulatta	ENSMMUG00000020666	3 retrocopies	retro_mmul_1298, retro_mmul_2143, retro_mmul_2246,
Monodelphis domestica	ENSMODG00000011783	2 retrocopies	retro_mdom_17, retro_mdom_884,
Mustela putorius furo	ENSMPUG00000009110	5 retrocopies	retro_mputfur_1263, retro_mputfur_1637, retro_mputfur_263, retro_mputfur_682, retro_mputfur_703,
Mus musculus	ENSMUSG00000091896	3 retrocopies	retro_mmus_2267, retro_mmus_27, retro_mmus_629,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Oryctolagus cuniculus	ENSOCUG00000029448	10 retrocopies	retro_ocun_1220, retro_ocun_1426, retro_ocun_1536, retro_ocun_1660, retro_ocun_1856, retro_ocun_1941, retro_ocun_261, retro_ocun_467, retro_ocun_887, retro_ocun_988,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pongo abelii	ENSPPYG00000015844	6 retrocopies	retro_pabe_1016, retro_pabe_1164, retro_pabe_1257, retro_pabe_2330, retro_pabe_30, retro_pabe_3670 ,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Pan troglodytes	ENSPTRG00000017303	3 retrocopies	retro_ptro_26, retro_ptro_3141, retro_ptro_341,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,
Tarsius syrichta	ENSTSYG00000005459	1 retrocopy	retro_tsyr_1421,