RetrogeneDB ID: retro_pabe_3614

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:14160721..14161308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E3
• Ensembl ID: ENSPPYG00000012987
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 3 [Source:HGNC Symbol;Acc:12479]

Sequence

>retro_pabe_3614
ATGTCCAGTGATAGGCAAAGGTCTGATGATGAGAGCCCCAGCACCAGCAGTGGCAGTTCAGATGCAGACCAGCCGCTCCA
GAGCCTGAAGAACAGGAGGAAAGAAAACCTTCTGCCACCCAGCAGAAGAAAAACACCAAACTCTCTAGCAAAACCACTGC
TAAGTTATCCACTAGTGCTAAAAGAATTCAGAAGGAGCTAGCTGAAATAACCCTTGATCCTCCTCCTAATTGCAGTGCTG
GGCCTAAAGGAGGTAACATTTATGAATGCAGATCAACTATACTTGGTCCACCAGGTTCTGTATATGAAAGTGGTGTGTTT
TTGCTGGATATCACATTTTCATCAGATTATCCATTTAAGCCACCAAAGGTTACTTTCCACACCAGAATCTATCACTGCAA
CATCAACAGTCAGGGAGTCATCTGTCTGGACATCCTTAAAGACAACTGGAGTCCCGCTTTGACTATTTCAAAGGTTTTGC
TGTCTATTTGTTCCCTTTTGACGGACTGCAACCCTGTGGATCCTCTAGTTGGAAGCATAGCCACTCAGTATTTGACCAAC
AGAGCAGCACACGACAAGATAGCCAAA

Alignment

ORF - retro_pabe_3614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.0 %
• Parental protein coverage: 96.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSDRQRSDDESPSTSSGSSDADQRD-PAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKE
          MSSDRQRSDDESPST...SS.....D.PAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKE
Retrocopy MSSDRQRSDDESPST---SSGSSDAD<PAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKE

Parental  LAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSSDYPFKPPKVTFRTRIYHCNIN
          LAEITLDPPPNCSAGPKG.NIYE.RSTILGPPGSVYE.GVF.LDITFSSDYPFKPPKVTF.TRIYHCNIN
Retrocopy LAEITLDPPPNCSAGPKGGNIYECRSTILGPPGSVYESGVFLLDITFSSDYPFKPPKVTFHTRIYHCNIN

Parental  SQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIAR
          SQGVICLDILKDNWSPALTISKVLLSICSLLTDCNP.DPLVGSIATQYLTNRA.HD.IA.
Retrocopy SQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPVDPLVGSIATQYLTNRAAHDKIAK

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	0.44 RPM	16.48 RPM
SRP007412_cerebellum	0.12 RPM	25.54 RPM
SRP007412_heart	0.09 RPM	9.09 RPM
SRP007412_kidney	0.46 RPM	19.06 RPM
SRP007412_liver	0.09 RPM	8.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3614 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3614 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3614 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4653
Pan troglodytes	retro_ptro_68
Gorilla gorilla	retro_ggor_76

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
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,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,