RetrogeneDB ID: retro_pabe_401

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:72467415..72467812(-)
• Located in intron of: ENSPPYG00000000473

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSPPYG00000015950
• Aliases: None
• Description: ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]

Sequence

>retro_pabe_401
CAGGTGGCTGAAGGAGAGAAATGTATTTGGTATCTGCCATATCTTTGCAACCTTCGGTGACACTTTTGTCCATGTCACTG
ATCTTTCTGGCAAAGAAACCATCTGCCGTGTGACTGGTGGGATGAAGGTAAAGGCAGACCGAGATGAATCCTTGCCATAT
GCTGCTTTGTTGGCTGCCCAGGATGTGGCCCAGAGGTGCAAGGAGCCAGGTGTCACTGCCCTACACATCAAACTCTGGGC
CACAGGAGGAAATAGGACCAAGACCCCTGGACCTGGGGCCAGTCGGCCTTCAGAACCCTTGCCCGCTTGAGTATGAAGAT
CAGGCAGATTGAGGACGTCACCCCCGTCCCCTCTTGACAGCACCCACAGGAAGTGGGGTCGCTGTGATCACCGTCTG

Alignment

ORF - retro_pabe_401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.96 %
• Parental protein coverage: 87.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QVAEGE-NVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESSPYAAMLAAQDVAQRCKEL
          QVAEGE.NVFG.CHIFA.F.DTFVHVTDLSGKETICRVTGGMKVKADRDES.PYAA.LAAQDVAQRCKE.
Retrocopy QVAEGE>NVFGICHIFATFGDTFVHVTDLSGKETICRVTGGMKVKADRDESLPYAALLAAQDVAQRCKEP

Parental  GITALHIKLRATGGNRTKTPGPGA-QSALRALARSGMKIGRIEDVTPIPS-DSTRRKGGRRGRRL
          G.TALHIKL.ATGGNRTKTPGPGA.QSA.R.LAR..MKI..IEDVTP.PS.DST.RK.GR...RL
Retrocopy GVTALHIKLWATGGNRTKTPGPGA<QSAFRTLARLSMKIRQIEDVTPVPS>DSTHRKWGRCDHRL

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	184.89 RPM
SRP007412_cerebellum	0.00 RPM	112.24 RPM
SRP007412_heart	0.12 RPM	182.79 RPM
SRP007412_kidney	0.13 RPM	315.29 RPM
SRP007412_liver	0.00 RPM	293.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_401 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_401 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_401 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_268
Pan troglodytes	retro_ptro_224
Gorilla gorilla	retro_ggor_316
Macaca mulatta	retro_mmul_570

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015004	1 retrocopy	retro_acar_201,
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Echinops telfairi	ENSETEG00000002899	6 retrocopies	retro_etel_1270, retro_etel_1358, retro_etel_1851, retro_etel_1995, retro_etel_293, retro_etel_967,
Homo sapiens	ENSG00000164587	8 retrocopies	retro_hsap_119, retro_hsap_1622, retro_hsap_268, retro_hsap_3001, retro_hsap_3113, retro_hsap_3232, retro_hsap_3495, retro_hsap_3789,
Gorilla gorilla	ENSGGOG00000024593	8 retrocopies	retro_ggor_1225, retro_ggor_2080, retro_ggor_2135, retro_ggor_2199, retro_ggor_222, retro_ggor_2362, retro_ggor_2548, retro_ggor_316,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Pongo abelii	ENSPPYG00000015950	7 retrocopies	retro_pabe_1340, retro_pabe_2487, retro_pabe_2571, retro_pabe_2888, retro_pabe_3204, retro_pabe_401 , retro_pabe_494,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Sarcophilus harrisii	ENSSHAG00000018052	3 retrocopies	retro_shar_380, retro_shar_381, retro_shar_503,
Tupaia belangeri	ENSTBEG00000006368	10 retrocopies	retro_tbel_1147, retro_tbel_1332, retro_tbel_1603, retro_tbel_1868, retro_tbel_202, retro_tbel_3517, retro_tbel_3619, retro_tbel_416, retro_tbel_519, retro_tbel_740,