RetrogeneDB ID: retro_pvam_393

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2911:162663..163521(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST13
• Ensembl ID: ENSPVAG00000011908
• Aliases: None
• Description: suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) [Source:HGNC Symbol;Acc:11343]

Sequence

>retro_pvam_393
GCAAAAGAAAATATAAAGACAGAAATTAACAGTGAAGATGTGATTGAACCACATGCCGAGCCCCTCAAGAAAAGGGAGAT
GAAAACGCAGAGATAACTGAAGAGATGATGGATCAGGCAAATGATAAAAAAGCGGCTGCCATTGATGCCCTGAGTGATGG
TGAACTACAGAAAGCCATTGACTTGTTCACTGATGCCGTCGGCCTGATTCTTACTTGGCCATTCTATATACCAAGAGAGC
CAGTGTCTTCATCAAATTACAGAAGCCAAATGCTGCCAGTCTATGACTGTGACAGAACTATTAAAATAAATCCTAATTCA
GCTCAGTCCTGCAAGTGATGAGGGAAAGCACAGACTTCTGGGCCACTGGGAAGAAGCATCCCATGATCTCGCCCTTGCAT
GTAAATTGGATTATGATGAAGATGCTAGGACAATGCTGAAAGAAGTTCAACCAAGTGCCTAGAAAATTGCAAAACGTCAG
AGAAAGTATGAGTGGAAACGTGAAGGAGAGAGATCAAAGAAAAAATTAAAAGGGTTAATTAAGAAGGTTTGGGGAGAACA
TGAGAGAGCCCAGAGGGAGGATGAAGCCAGATGACAATCAGGAGCTCAGTAGAGTTCTTTTCCAGGCGGCTTTCTTGGGG
GAACGCCTGGAATGGGAGGGAGCATGCTTCGAATGACAGGAATGCCTGGGCTCAGTGAAATTCTTAGTGATCCAAAGGTT
CTTGCCATGCAGGATCCAGAAGTTATGGTGGCCTTCCAGGATGTGGCTCAGAACCTGGCAAATATGTCAAAATATCAGAG
CAACCCAAAGATTATGAATCACATCAGTAAATTGTCAGCCAAATTTGGAGGTCAAGCA

Alignment

ORF - retro_pvam_393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.0 %
• Parental protein coverage: 79.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SSEESDLEIDNEGVIEPDTD-APQEMGDENVEITEEMMDQANDKKGAAIDALNDGELQKAIDLFTDAIKL
          ..E....EI..E.VIEP....APQE.GDEN.EITEEMMDQANDKK.AAIDAL.DGELQKAIDLFTDA..L
Retrocopy AKENIKTEINSEDVIEPHAE<APQEKGDENAEITEEMMDQANDKKAAAIDALSDGELQKAIDLFTDAVGL

Parental  -NPRLAILYAKRASVFIKLQKPNAA-IRDCDRAIEINPDSAQ-PYKWRGKAHRLLGHWEEAAHDLALACK
          ....LAILY.KRASVFIKLQKPNAA...DCDR.I.INP.SAQ.P....GK.HRLLGHWEEA.HDLALACK
Retrocopy <DSYLAILYTKRASVFIKLQKPNAA>VYDCDRTIKINPNSAQ>PASDEGK-HRLLGHWEEASHDLALACK

Parental  LDYDEDASAMLKEVQPRAQKIAEHRRKYERKREEREIKERMERVKKAREEHERAQREEEARRQSGA-QYG
          LDYDEDA..MLKEVQP.A.KIA....K..RK.E.....ER.....K..........E...R......Q.G
Retrocopy LDYDEDARTMLKEVQPSA*KIA----KRQRKYEWKREGERSKKKLKGLIKKVWGEHERAQREDEAR*QSG

Parental  SFPGGFPGGMPGNFPGGMPGMGGAMPGMAGMPGLNEILSDPEVLAAMQDPEVMVAFQDVAQNPANMSKYQ
          .....FPGG....F.GG.PGMGG.M..M.GMPGL.EILSDP.VL.AMQDPEVMVAFQDVAQN.ANMSKYQ
Retrocopy AQ*SSFPGG----FLGGTPGMGGSMLRMTGMPGLSEILSDPKVL-AMQDPEVMVAFQDVAQNLANMSKYQ

Parental  SNPKVMNLISKLSAKFGGQA
          SNPK.MN.ISKLSAKFGGQA
Retrocopy SNPKIMNHISKLSAKFGGQA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_393 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 127 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005227	1 retrocopy	retro_acar_2,
Ailuropoda melanoleuca	ENSAMEG00000013880	1 retrocopy	retro_amel_135,
Bos taurus	ENSBTAG00000006202	4 retrocopies	retro_btau_254, retro_btau_427, retro_btau_621, retro_btau_658,
Canis familiaris	ENSCAFG00000001139	14 retrocopies	retro_cfam_1029, retro_cfam_1101, retro_cfam_1122, retro_cfam_1239, retro_cfam_1467, retro_cfam_1830, retro_cfam_1950, retro_cfam_1958, retro_cfam_247, retro_cfam_262, retro_cfam_582, retro_cfam_808, retro_cfam_901, retro_cfam_969,
Choloepus hoffmanni	ENSCHOG00000012676	1 retrocopy	retro_chof_2222,
Callithrix jacchus	ENSCJAG00000004644	11 retrocopies	retro_cjac_1843, retro_cjac_1953, retro_cjac_2177, retro_cjac_2275, retro_cjac_2789, retro_cjac_3123, retro_cjac_3570, retro_cjac_4019, retro_cjac_488, retro_cjac_640, retro_cjac_685,
Cavia porcellus	ENSCPOG00000002290	4 retrocopies	retro_cpor_1394, retro_cpor_1477, retro_cpor_166, retro_cpor_961,
Felis catus	ENSFCAG00000011847	2 retrocopies	retro_fcat_920, retro_fcat_987,
Homo sapiens	ENSG00000100380	16 retrocopies	retro_hsap_1055, retro_hsap_1203, retro_hsap_178, retro_hsap_201, retro_hsap_2078, retro_hsap_2189, retro_hsap_2853, retro_hsap_3206, retro_hsap_3907, retro_hsap_4009, retro_hsap_4876, retro_hsap_500, retro_hsap_619, retro_hsap_756, retro_hsap_812, retro_hsap_986,
Gorilla gorilla	ENSGGOG00000026747	16 retrocopies	retro_ggor_1600, retro_ggor_1734, retro_ggor_1791, retro_ggor_1975, retro_ggor_2177, retro_ggor_2634, retro_ggor_2692, retro_ggor_277, retro_ggor_3045, retro_ggor_629, retro_ggor_666, retro_ggor_749, retro_ggor_788, retro_ggor_832, retro_ggor_833, retro_ggor_938,
Microcebus murinus	ENSMICG00000008875	2 retrocopies	retro_mmur_481, retro_mmur_954,
Myotis lucifugus	ENSMLUG00000007764	2 retrocopies	retro_mluc_1088, retro_mluc_2021,
Macaca mulatta	ENSMMUG00000019118	3 retrocopies	retro_mmul_1842, retro_mmul_402, retro_mmul_438,
Monodelphis domestica	ENSMODG00000013042	2 retrocopies	retro_mdom_1087, retro_mdom_31,
Mus musculus	ENSMUSG00000022403	2 retrocopies	retro_mmus_2997, retro_mmus_651,
Nomascus leucogenys	ENSNLEG00000015378	17 retrocopies	retro_nleu_1142, retro_nleu_1155, retro_nleu_1606, retro_nleu_1852, retro_nleu_2075, retro_nleu_2088, retro_nleu_2376, retro_nleu_2404, retro_nleu_247, retro_nleu_2555, retro_nleu_2765, retro_nleu_3121, retro_nleu_3122, retro_nleu_319, retro_nleu_447, retro_nleu_552, retro_nleu_988,
Otolemur garnettii	ENSOGAG00000016932	1 retrocopy	retro_ogar_224,
Pongo abelii	ENSPPYG00000011858	14 retrocopies	retro_pabe_1004, retro_pabe_2181, retro_pabe_2361, retro_pabe_2657, retro_pabe_2885, retro_pabe_3183, retro_pabe_3673, retro_pabe_3794, retro_pabe_437, retro_pabe_554, retro_pabe_727, retro_pabe_763, retro_pabe_798, retro_pabe_880,
Pteropus vampyrus	ENSPVAG00000011908	2 retrocopies	retro_pvam_1104, retro_pvam_393 ,
Rattus norvegicus	ENSRNOG00000019070	8 retrocopies	retro_rnor_1360, retro_rnor_1725, retro_rnor_1798, retro_rnor_1976, retro_rnor_2204, retro_rnor_2372, retro_rnor_2481, retro_rnor_2543,
Sarcophilus harrisii	ENSSHAG00000000319	2 retrocopies	retro_shar_70, retro_shar_767,
Sus scrofa	ENSSSCG00000000071	1 retrocopy	retro_sscr_428,
Ictidomys tridecemlineatus	ENSSTOG00000003165	1 retrocopy	retro_itri_88,