RetrogeneDB ID: retro_pabe_33

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:57618949..57619726(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020403
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SPIN1
• Ensembl ID: ENSPPYG00000019355
• Aliases: SPIN1, SPIN, Spindlin-1
• Description: Spindlin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R997]

Sequence

>retro_pabe_33
ATGAAGACCCCGTTTGGAAAGGCAGCTGCAGGGCAGCGGTCCAGGACAGGCGCTGGCCACGGCAGTGTGTCTGTTACCAT
GATAAAGAGGAAGGCTGCACACAAGAAGCATAGGAGCCGACCCACCTCCCAGCCTCGGAGGAACATCGTGGGCTGCAGAA
TTCAGCACGGATGGAAAGATGGAGATGAACCTCTAACACAGTGGAAAGGAACCGTTCTGGATCAGGTACCTGTAAATCCC
TCTCTGTATCTTATCAAATATGATGGATTTGACTGTGTTTATGGATTGGAACTTCACAGAGATGAAAGAGTGTCATCACT
TGAAGTCCTTCCTAATAGAGTTGCATCATCTAGAATCAGTGATACACACTTGGCAGAAATAATGGTTGGCAAAGCAGTGG
AACATATTTTTGAGACAGAGGAAGGTTCCAAAAATGAATGGAGGGGGATGGTCTTAGCTCAGGCACCTGTCATGAACACA
TGGTTTTACATTACCTATGAGAAAGATCCTGTATTATATATGTACCAGCTCTTAGATGATTATAAAGATGGTGACCTCCG
CATCCTTCAAGATTCCAATGATTCTCCTCTGGCAGAGAGGGAGCCAGGAGAAGTCATAGACAGCCTGGTAGGCAAACAGG
TGGAATACGCCAAAGACGATGGCTCCAAGAGAACTGGCATGGTCATTCATCAGGTAGAAGCAAAACCCTCTGTGTACTTC
ATCAAATTTGATGATGATTTCCATATCTATGTCTACGATTTGGTAAAAACATCTTAG

Alignment

ORF - retro_pabe_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKTPFGKTPGQRSRADAGHAGVSANMMKKRTSHKKHRSSVGPSKPVSQPRRNIVGCRIQHGWKEGNGPVT
          MKTPF....G..........G.............K.......S.P.SQPRRNIVGCRIQHGWK.G..P.T
Retrocopy MKTPF----GKAAAGQRSRTGAGHGSVSVTMIKRKAAHKKHRSRPTSQPRRNIVGCRIQHGWKDGDEPLT

Parental  QWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHM
          QWKGTVLDQVPVNPSLYLIKYDGFDCVYGLEL..DERVS.LEVLP.RVA.SRISD.HLA..M.GKAVEH.
Retrocopy QWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELHRDERVSSLEVLPNRVASSRISDTHLAEIMVGKAVEHI

Parental  FETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVV
          FETE.GSK.EWRGMVLA.APVMNTWFYITYEKDPVLYMYQLLDDYK.GDLRI..DSNDSP.AEREPGEV.
Retrocopy FETEEGSKNEWRGMVLAQAPVMNTWFYITYEKDPVLYMYQLLDDYKDGDLRILQDSNDSPLAEREPGEVI

Parental  DSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS
          DSLVGKQVEYAK.DGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS
Retrocopy DSLVGKQVEYAKDDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

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	3.15 RPM	129.88 RPM
SRP007412_cerebellum	4.86 RPM	82.20 RPM
SRP007412_heart	0.60 RPM	23.36 RPM
SRP007412_kidney	0.99 RPM	58.50 RPM
SRP007412_liver	0.89 RPM	19.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_33 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_33 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003301	4 retrocopies	retro_amel_1831, retro_amel_1879, retro_amel_38, retro_amel_41,
Bos taurus	ENSBTAG00000003044	4 retrocopies	retro_btau_1678, retro_btau_1841, retro_btau_187, retro_btau_553,
Canis familiaris	ENSCAFG00000002208	3 retrocopies	retro_cfam_153, retro_cfam_2095, retro_cfam_59,
Choloepus hoffmanni	ENSCHOG00000006983	2 retrocopies	retro_chof_1343, retro_chof_1852,
Callithrix jacchus	ENSCJAG00000017452	1 retrocopy	retro_cjac_227,
Cavia porcellus	ENSCPOG00000000743	1 retrocopy	retro_cpor_123,
Echinops telfairi	ENSETEG00000013719	1 retrocopy	retro_etel_28,
Felis catus	ENSFCAG00000007197	2 retrocopies	retro_fcat_32, retro_fcat_70,
Homo sapiens	ENSG00000106723	1 retrocopy	retro_hsap_64,
Loxodonta africana	ENSLAFG00000027497	2 retrocopies	retro_lafr_18, retro_lafr_58,
Microcebus murinus	ENSMICG00000014510	1 retrocopy	retro_mmur_8,
Myotis lucifugus	ENSMLUG00000008516	2 retrocopies	retro_mluc_132, retro_mluc_1626,
Mustela putorius furo	ENSMPUG00000008585	1 retrocopy	retro_mputfur_139,
Mus musculus	ENSMUSG00000021395	3 retrocopies	retro_mmus_112, retro_mmus_16, retro_mmus_3351,
Oryctolagus cuniculus	ENSOCUG00000011880	1 retrocopy	retro_ocun_63,
Otolemur garnettii	ENSOGAG00000002166	2 retrocopies	retro_ogar_2327, retro_ogar_9,
Procavia capensis	ENSPCAG00000015800	1 retrocopy	retro_pcap_14,
Pongo abelii	ENSPPYG00000019355	1 retrocopy	retro_pabe_33 ,
Pan troglodytes	ENSPTRG00000021088	2 retrocopies	retro_ptro_116, retro_ptro_95,
Pteropus vampyrus	ENSPVAG00000013391	3 retrocopies	retro_pvam_2, retro_pvam_22, retro_pvam_858,
Rattus norvegicus	ENSRNOG00000011119	4 retrocopies	retro_rnor_1483, retro_rnor_1531, retro_rnor_281, retro_rnor_2818,
Ictidomys tridecemlineatus	ENSSTOG00000029107	1 retrocopy	retro_itri_136,
Tursiops truncatus	ENSTTRG00000005602	6 retrocopies	retro_ttru_1061, retro_ttru_13, retro_ttru_1452, retro_ttru_1506, retro_ttru_1669, retro_ttru_1698,