RetrogeneDB ID: retro_ptro_2085

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:123338227..123338759(-)
• Located in intron of: ENSPTRG00000016403

Retrocopy information

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

Parental gene information

• Parental gene symbol: SET
• Ensembl ID: ENSPTRG00000021436
• Aliases: None
• Description: None

Sequence

>retro_ptro_2085
AAGCACAGGGATGTTGCACAAATTGAAATAGACAGACTTTACAAACAAGCCAGTGAGGAAATTTCCAAAGTAGAACAAAA
ATGTAACAAACTTCAAACTATTTAAAAGAGGTTGTAATTGATCTCCTGAATTTCAAATTTAGAGGTACTGTTAATCAACT
ATGTGCAAGTGACTTCCCTGCTTGAAATGCGAATGAAGAGATGCTGTGCTATCTCTTTAGAATGAAAGTGACAGAATTTA
AAGATATTAAATGATATTATAGAATAGATTTTTATTTTGCTGAAAAACCTTATTTTAAAATAAAGTTCCTCGCAACAAAT
TTCATCTCAAGTAGAGTGGTGGCCCATCTTCAGTGTTGACTAAAGTTAAATGGGAATCTGAGAAGGACTTGATTAAATGA
TCATGTCAGAAGTAAAATAAAGCTGTCTAGAAGAGGAAGCATGAAAAATCTCAGGCCTTCTTCACTTGATTCACCAATGA
TTCTGATGCAGGTGCAGGTGAATTAAGAGAGCTCATCAAAGTTGCTCTTTGG

Alignment

ORF - retro_ptro_2085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.74 %
• Parental protein coverage: 62.41 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EHIDEVQNEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLG-EEDE
          .H.D..Q.EIDRL..QASEEI.KVEQK.NKL......KR..LI..I.N..V....N..QV..LL.....E
Retrocopy KHRDVAQIEIDRLYKQASEEISKVEQKCNKLQT--I*KRL*LIS*ISNLEVL-LINYVQVTSLLE<NANE

Parental  EALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFE-NKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRS
          E.L.YL.R..VTEF.DIK..YRIDFYF.E.PYF..NKV....FHL..SG.PSS..T..KW.S.KDL.K.S
Retrocopy EMLCYLFRMKVTEFKDIK*YYRIDFYFAEKPYFK<NKVPRNKFHLK*SGGPSSVLTKVKWESEKDLIK*S

Parental  SQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIW
          .Q..NKA..KR.HE....FFT.FT..SDAGA.EL.E.IK...W
Retrocopy CQK*NKAV*KRKHEKSQAFFT*FTNDSDAGAGELRELIKVALW

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	0.09 RPM	127.28 RPM
SRP007412_cerebellum	0.00 RPM	105.86 RPM
SRP007412_heart	0.00 RPM	94.58 RPM
SRP007412_kidney	0.00 RPM	106.44 RPM
SRP007412_liver	0.00 RPM	75.78 RPM
SRP007412_testis	0.00 RPM	73.45 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2085 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2085 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3088
Pongo abelii	retro_pabe_2557
Equus caballus	retro_ecab_505

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 136 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris	ENSCAFG00000032728	2 retrocopies	retro_cfam_47, retro_cfam_83,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Microcebus murinus	ENSMICG00000017643	2 retrocopies	retro_mmur_1398, retro_mmur_775,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Mus musculus	ENSMUSG00000054766	17 retrocopies	retro_mmus_1366, retro_mmus_1435, retro_mmus_1671, retro_mmus_1743, retro_mmus_2329, retro_mmus_2448, retro_mmus_2484, retro_mmus_2664, retro_mmus_2665, retro_mmus_3015, retro_mmus_3290, retro_mmus_345, retro_mmus_3513, retro_mmus_517, retro_mmus_887, retro_mmus_929, retro_mmus_967,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus	ENSOCUG00000007501	12 retrocopies	retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Pan troglodytes	ENSPTRG00000021436	16 retrocopies	retro_ptro_1232, retro_ptro_1836, retro_ptro_1838, retro_ptro_2073, retro_ptro_2085 , retro_ptro_209, retro_ptro_2151, retro_ptro_2152, retro_ptro_225, retro_ptro_2283, retro_ptro_2965, retro_ptro_3140, retro_ptro_321, retro_ptro_561, retro_ptro_913, retro_ptro_953,
Pteropus vampyrus	ENSPVAG00000003437	2 retrocopies	retro_pvam_1198, retro_pvam_886,
Ictidomys tridecemlineatus	ENSSTOG00000010546	6 retrocopies	retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,
Tursiops truncatus	ENSTTRG00000011605	7 retrocopies	retro_ttru_1433, retro_ttru_1600, retro_ttru_181, retro_ttru_1901, retro_ttru_537, retro_ttru_919, retro_ttru_931,