RetrogeneDB ID: retro_ptro_2112

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:175593484..175593941(-)
• Located in intron of: ENSPTRG00000016595

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2N
• Ensembl ID: ENSPTRG00000005297
• Aliases: None
• Description: None

Sequence

>retro_ptro_2112
ATGGCTGGGCTGCCCAGCAGGATCGTCAAGGAAACCCAGCGTTTGCTGGCAGAACCAGTTCCTGGCCTCAAAGCAGAACC
ATATGAGAGCAACACCCATTATTTTCATGTGGTCATTGCCAGTCCCTGGGATTCCCACTGTGAGGGAGGGACTTTTAAAC
TTGGACTATTTCTTCCAGAAGAATACCCAATGGCAGCCCCTAAAGTGCGTTTTATGACCAAAATTTGTCATCCTAATGTA
GACAAGTTGGGAAGAATATGTTAAGATATTTTGAAAGGTAAGTGGTCCCCAGCCCTGAAGATCCGCACAGTTCTGCTATG
GATCCAGGCCTTGTTAAGTGCTCCAAATCCAGATGATCCATTAGCAAATGATGCAGAGGAGCAGTGGAAACACCAACGAA
GCCCAAGCCATATAAACAGCTAGAGCAGGGACTAGGCTATATGCCATGAATAATATT

Alignment

ORF - retro_ptro_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVR
          MAGLP.RI.KETQRLLAEPVPG.KAEP.ESN..YFHVVIA.P.DS..EGGTFKL.LFLPEEYPMAAPKVR
Retrocopy MAGLPSRIVKETQRLLAEPVPGLKAEPYESNTHYFHVVIASPWDSHCEGGTFKLGLFLPEEYPMAAPKVR

Parental  FMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWK-TNEAQAIET
          FMTKI.HPNVDKLGRIC.DILK.KWSPAL.IRTVLL.IQALLSAPNPDDPLAND..EQWK.TNEAQAI.T
Retrocopy FMTKICHPNVDKLGRIC*DILKGKWSPALKIRTVLLWIQALLSAPNPDDPLANDAEEQWK>TNEAQAI*T

Parental  ARAWTRLYAMNNI
          ARA.TRLYAMNNI
Retrocopy ARAGTRLYAMNNI

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	0.05 RPM	63.62 RPM
SRP007412_cerebellum	0.00 RPM	40.76 RPM
SRP007412_heart	0.00 RPM	23.81 RPM
SRP007412_kidney	0.00 RPM	28.56 RPM
SRP007412_liver	0.00 RPM	18.04 RPM
SRP007412_testis	0.00 RPM	149.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2112 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2112 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3124
Pongo abelii	retro_pabe_2580

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 104 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009833	1 retrocopy	retro_amel_507,
Bos taurus	ENSBTAG00000021767	2 retrocopies	retro_btau_1173, retro_btau_1614,
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Dasypus novemcinctus	ENSDNOG00000018952	9 retrocopies	retro_dnov_1002, retro_dnov_1066, retro_dnov_1107, retro_dnov_1185, retro_dnov_1487, retro_dnov_1977, retro_dnov_2598, retro_dnov_277, retro_dnov_492,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Felis catus	ENSFCAG00000004260	2 retrocopies	retro_fcat_1477, retro_fcat_1598,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Microcebus murinus	ENSMICG00000014081	4 retrocopies	retro_mmur_1351, retro_mmur_220, retro_mmur_267, retro_mmur_611,
Myotis lucifugus	ENSMLUG00000009982	2 retrocopies	retro_mluc_2166, retro_mluc_453,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Mus musculus	ENSMUSG00000074781	6 retrocopies	retro_mmus_1031, retro_mmus_2656, retro_mmus_3031, retro_mmus_3294, retro_mmus_3510, retro_mmus_524,
Nomascus leucogenys	ENSNLEG00000005695	2 retrocopies	retro_nleu_1078, retro_nleu_2279,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Otolemur garnettii	ENSOGAG00000034461	7 retrocopies	retro_ogar_1502, retro_ogar_2178, retro_ogar_406, retro_ogar_408, retro_ogar_566, retro_ogar_584, retro_ogar_732,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112 , retro_ptro_3253, retro_ptro_956,
Sorex araneus	ENSSARG00000005945	3 retrocopies	retro_sara_174, retro_sara_438, retro_sara_695,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Sus scrofa	ENSSSCG00000000908	4 retrocopies	retro_sscr_101, retro_sscr_369, retro_sscr_698, retro_sscr_699,
Tupaia belangeri	ENSTBEG00000012497	10 retrocopies	retro_tbel_108, retro_tbel_1208, retro_tbel_1235, retro_tbel_1727, retro_tbel_2393, retro_tbel_2732, retro_tbel_275, retro_tbel_3151, retro_tbel_4655, retro_tbel_849,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,
Tursiops truncatus	ENSTTRG00000003311	3 retrocopies	retro_ttru_1235, retro_ttru_286, retro_ttru_702,