RetrogeneDB ID: retro_pabe_233

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:35411883..35412564(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3S1
• Ensembl ID: ENSPPYG00000015700
• Aliases: None
• Description: adaptor-related protein complex 3, sigma 1 subunit [Source:HGNC Symbol;Acc:2013]

Sequence

>retro_pabe_233
GGAGGCGGGTGGGGAAGAGTCACCGGCGAGATTACTAGGCAAGGCTTGTGCGCCCGCTCCCGCCCTGGCCCCCAGTGCCC
ACCTAGTCAGCCCAGCACAGCCATGATCAAGGCGATCCTAATCTTCAACAACCACGGGAAGCCGTGGCTCTCCAAGTTCT
ACCAGCCCTACAGTGAAGATACACAACAGCAAATCATCAGGGAGACTTTCCATTTGGTATCTAAGAGAGATGAAAATGTT
TGTAATTTCCTAGAAGGGGGATTATTAATTGGAGGATCTGAGAACAAACTGATTTATAGACATTACGCAACGATATATTT
TGTCTTCTATGTGGATTCTTCAGAAAGTGAACTTGGCATTTTAGATCTAATTCAAGTATTTGTGGAAACATTAGACAAAT
GTTTTGAAAATGTCTGTGAACTGGATTTGATCTTCCATGTAGACAAGGTTCACAATATTCTTGCAGAAATAATGATGAGG
AGAATGGTATTGGAGACAAACATGAATCAGATTGTTACACAAATTGATGCATAAAATAAGCTGGAAAAATCTGAGGCTGG
CTTAGCGGGAGCCCCAGTCCGTGCTGTATCAGCTGTAAAGAATATGAATTTTCCTGAGATCCCAAGAAATATTGACATTG
GTGACATCAGTATAAAAGTGCCAAACCTGCCCTCTTTTAAA

Alignment

ORF - retro_pabe_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 77.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGGWGRIAGEITRRGLRARPRPGPQCPPGRPGTAMIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETF
          GGGWGR..GEITR.GL.AR.RPGPQCPP..P.TAMIKAILIFNNHGKP.LSKFYQPYSEDTQQQIIRETF
Retrocopy GGGWGRVTGEITRQGLCARSRPGPQCPPSQPSTAMIKAILIFNNHGKPWLSKFYQPYSEDTQQQIIRETF

Parental  HLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCE
          HLVSKRDENVCNFLEGGLLIGGS.NKLIYRHYAT.YFVF.VDSSESELGILDLIQVFVETLDKCFENVCE
Retrocopy HLVSKRDENVCNFLEGGLLIGGSENKLIYRHYATIYFVFYVDSSESELGILDLIQVFVETLDKCFENVCE

Parental  LDLIFHVDKVHNILAEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAGLAGAPARAVSAVKNMNLPEIPRN
          LDLIFHVDKVHNILAE..M..MVLETNMN.IVTQIDA.NKLEKSEAGLAGAP.RAVSAVKNMN.PEIPRN
Retrocopy LDLIFHVDKVHNILAEIMMRRMVLETNMNQIVTQIDA*NKLEKSEAGLAGAPVRAVSAVKNMNFPEIPRN

Parental  INIGDISIKVPNLPSFK
          I.IGDISIKVPNLPSFK
Retrocopy IDIGDISIKVPNLPSFK

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	22.72 RPM
SRP007412_cerebellum	0.00 RPM	25.66 RPM
SRP007412_heart	0.00 RPM	6.65 RPM
SRP007412_kidney	0.00 RPM	14.05 RPM
SRP007412_liver	0.03 RPM	11.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_233 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_233 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000203	1 retrocopy	retro_cfam_790,
Callithrix jacchus	ENSCJAG00000016767	1 retrocopy	retro_cjac_1143,
Cavia porcellus	ENSCPOG00000007192	3 retrocopies	retro_cpor_1528, retro_cpor_551, retro_cpor_779,
Felis catus	ENSFCAG00000029920	3 retrocopies	retro_fcat_1434, retro_fcat_151, retro_fcat_680,
Homo sapiens	ENSG00000177879	3 retrocopies	retro_hsap_1084, retro_hsap_3563, retro_hsap_507,
Gorilla gorilla	ENSGGOG00000016895	2 retrocopies	retro_ggor_467, retro_ggor_856,
Loxodonta africana	ENSLAFG00000015311	1 retrocopy	retro_lafr_12,
Macropus eugenii	ENSMEUG00000010623	1 retrocopy	retro_meug_969,
Microcebus murinus	ENSMICG00000006157	4 retrocopies	retro_mmur_1154, retro_mmur_399, retro_mmur_436, retro_mmur_851,
Myotis lucifugus	ENSMLUG00000002769	2 retrocopies	retro_mluc_1872, retro_mluc_504,
Macaca mulatta	ENSMMUG00000015288	2 retrocopies	retro_mmul_1821, retro_mmul_843,
Mustela putorius furo	ENSMPUG00000000782	1 retrocopy	retro_mputfur_1372,
Mus musculus	ENSMUSG00000024480	4 retrocopies	retro_mmus_1541, retro_mmus_3155, retro_mmus_3177, retro_mmus_3599,
Otolemur garnettii	ENSOGAG00000032376	1 retrocopy	retro_ogar_1005,
Ochotona princeps	ENSOPRG00000009176	2 retrocopies	retro_opri_1040, retro_opri_750,
Pongo abelii	ENSPPYG00000015700	2 retrocopies	retro_pabe_232, retro_pabe_233 ,
Pan troglodytes	ENSPTRG00000017155	5 retrocopies	retro_ptro_1119, retro_ptro_2113, retro_ptro_2420, retro_ptro_379, retro_ptro_736,
Pteropus vampyrus	ENSPVAG00000006575	3 retrocopies	retro_pvam_1196, retro_pvam_1232, retro_pvam_422,
Rattus norvegicus	ENSRNOG00000003829	1 retrocopy	retro_rnor_1460,
Sarcophilus harrisii	ENSSHAG00000001176	2 retrocopies	retro_shar_143, retro_shar_267,
Ictidomys tridecemlineatus	ENSSTOG00000011759	1 retrocopy	retro_itri_862,
Tupaia belangeri	ENSTBEG00000004775	7 retrocopies	retro_tbel_1449, retro_tbel_154, retro_tbel_1662, retro_tbel_2402, retro_tbel_2641, retro_tbel_3400, retro_tbel_4179,
Tarsius syrichta	ENSTSYG00000013231	9 retrocopies	retro_tsyr_1099, retro_tsyr_1234, retro_tsyr_1354, retro_tsyr_1431, retro_tsyr_1862, retro_tsyr_1960, retro_tsyr_58, retro_tsyr_941, retro_tsyr_949,
Tursiops truncatus	ENSTTRG00000000813	3 retrocopies	retro_ttru_1048, retro_ttru_1183, retro_ttru_145,