RetrogeneDB ID: retro_sscr_1089

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL893305.1:60320..60569(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO3
• Ensembl ID: ENSSSCG00000024026
• Aliases: None
• Description: small ubiquitin-like modifier 3 [Source:HGNC Symbol;Acc:11124]

Sequence

>retro_sscr_1089
AAAGAAAAGCCCAAGGAAGGAGTTAAGGCTGAGAACAATAATCAAACTAATCTGAAGATGGCAGGGATGGTTCTGTGGTG
CAGTTTAAGATTAAGAGACAAACAACACTTAGTAAACTAATGAAAGCCTACTGTGAATGACAAGAGTTTGTCAAGGAGGA
AAATCTGATTCCAAACTGATAGTCAGCCAATCAATGAAACAGACACACCAGCAGAGTTGGAAATAAAAGATGAAGATGCA
ATCGATGTA

Alignment

ORF - retro_sscr_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.24 %
• Parental protein coverage: 79.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEKPKEGVKTENDH-INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQ-GLSMRQIRFRFDGQPINEAD
          .EKPKEGVK.EN....N....G.DGSVVQFKIKR.T.LSKLMKAYCE.Q..LS.R.I.F..D.QPINE.D
Retrocopy KEKPKEGVKAENNN<SN*SEDGRDGSVVQFKIKRQTTLSKLMKAYCE*Q>SLSRRKI*FQTDSQPINETD

Parental  TPAQLEMEDEDTIDV
          TPA.LE..DED.IDV
Retrocopy TPAELEIKDEDAIDV

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
SRP014902_placenta	0.00 RPM	122.64 RPM
SRP014902_testis	0.00 RPM	86.00 RPM
SRP018288_heart	0.00 RPM	19.44 RPM
SRP018288_kidney	0.00 RPM	72.20 RPM
SRP018288_liver	0.00 RPM	66.20 RPM
SRP018288_lung	0.00 RPM	47.45 RPM
SRP018856_adipose	0.00 RPM	54.81 RPM
SRP035408_brain	0.00 RPM	121.80 RPM
SRP035408_liver	0.00 RPM	68.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1089 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1089 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_260

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002071	3 retrocopies	retro_amel_1388, retro_amel_1586, retro_amel_1863,
Bos taurus	ENSBTAG00000017321	3 retrocopies	retro_btau_1730, retro_btau_580, retro_btau_701,
Bos taurus	ENSBTAG00000030169	8 retrocopies	retro_btau_1047, retro_btau_1484, retro_btau_1804, retro_btau_260, retro_btau_344, retro_btau_489, retro_btau_582, retro_btau_895,
Callithrix jacchus	ENSCJAG00000010529	20 retrocopies	retro_cjac_1110, retro_cjac_1128, retro_cjac_1525, retro_cjac_1752, retro_cjac_1938, retro_cjac_1957, retro_cjac_1993, retro_cjac_2460, retro_cjac_2481, retro_cjac_2616, retro_cjac_2651, retro_cjac_2886, retro_cjac_2899, retro_cjac_2985, retro_cjac_3088, retro_cjac_3137, retro_cjac_4123, retro_cjac_711, retro_cjac_771, retro_cjac_774,
Felis catus	ENSFCAG00000026550	4 retrocopies	retro_fcat_1210, retro_fcat_1947, retro_fcat_823, retro_fcat_836,
Microcebus murinus	ENSMICG00000011011	2 retrocopies	retro_mmur_179, retro_mmur_41,
Myotis lucifugus	ENSMLUG00000025342	4 retrocopies	retro_mluc_1502, retro_mluc_272, retro_mluc_340, retro_mluc_625,
Myotis lucifugus	ENSMLUG00000028601	2 retrocopies	retro_mluc_1321, retro_mluc_2494,
Macaca mulatta	ENSMMUG00000006760	3 retrocopies	retro_mmul_2131, retro_mmul_2215, retro_mmul_47,
Mustela putorius furo	ENSMPUG00000010234	1 retrocopy	retro_mputfur_1504,
Mustela putorius furo	ENSMPUG00000013954	9 retrocopies	retro_mputfur_1086, retro_mputfur_1403, retro_mputfur_1535, retro_mputfur_273, retro_mputfur_275, retro_mputfur_385, retro_mputfur_666, retro_mputfur_948, retro_mputfur_995,
Oryctolagus cuniculus	ENSOCUG00000021739	4 retrocopies	retro_ocun_1024, retro_ocun_1631, retro_ocun_1690, retro_ocun_321,
Rattus norvegicus	ENSRNOG00000038489	1 retrocopy	retro_rnor_2158,
Sus scrofa	ENSSSCG00000017212	15 retrocopies	retro_sscr_1112, retro_sscr_1132, retro_sscr_1147, retro_sscr_1148, retro_sscr_123, retro_sscr_249, retro_sscr_277, retro_sscr_409, retro_sscr_591, retro_sscr_684, retro_sscr_754, retro_sscr_765, retro_sscr_814, retro_sscr_847, retro_sscr_969,
Sus scrofa	ENSSSCG00000024026	2 retrocopies	retro_sscr_1089 , retro_sscr_320,
Ictidomys tridecemlineatus	ENSSTOG00000010587	2 retrocopies	retro_itri_116, retro_itri_1259,
Ictidomys tridecemlineatus	ENSSTOG00000024685	10 retrocopies	retro_itri_1017, retro_itri_1123, retro_itri_1355, retro_itri_202, retro_itri_264, retro_itri_272, retro_itri_79, retro_itri_921, retro_itri_981, retro_itri_983,
Takifugu rubripes	ENSTRUG00000014892	1 retrocopy	retro_trub_25,