RetrogeneDB ID: retro_sscr_319

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:67799801..67800270(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2I
• Ensembl ID: ENSSSCG00000021560
• Aliases: UBE2I, UBC9
• Description: ubiquitin-conjugating enzyme E2I [Source:HGNC Symbol;Acc:12485]

Sequence

>retro_sscr_319
ATGTTGGGGATCACCCTCAGTAGACTCGCCCAGGAGAGGAAAGCTTGGAGGAAAGACCATCCATTTGGTTTCATGGCTGC
CCCTACAAAAAACCCCCAGGGCACAATGAACCTCATGAACTGGGAAAGCGCCATTCCTGGGAAGAAGGGGACTCTGTGGG
AGGGAGGCTTGTTTAAACTACGGGTGCTGTTCAAAGATGAATGTCCATCCTCACCATCGAAATGCAAGTTCAAGCCGTCC
TTACTTCACCCAAACCTGTACTCTTAAGGCTGGGTGTGCCTGTCCATCCTGGAGAACAAGGACTGGAGGCCAGCATCATG
ATTAAGCAGATCTTTTTAGGAATAAGGGAACTTCTAAATGAACCAAATACCCAAACTCCAGCTCAAGCAGAGGCCTACAT
GATCTACTGTCAAGACAGAGTGGAATACAAGAAAAGGTTCGAGTACAAGCCAAGAAGTTTGCTCTCTCA

Alignment

ORF - retro_sscr_319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPS
          M.GI.LSRLAQERKAWRKDHPFGF.A.PTKNP.GTMNLMNWE.AIPGKKGT.WEGGLFKLR.LFKD..PS
Retrocopy MLGITLSRLAQERKAWRKDHPFGFMAAPTKNPQGTMNLMNWESAIPGKKGTLWEGGLFKLRVLFKDECPS

Parental  SPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPA-ITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQ
          SP.KCKF.P.L.HPN.Y..G.VCLSIL.E.KDWRPA.I.IKQI.LGI.ELLNEPN.Q.PAQAEAY.IYCQ
Retrocopy SPSKCKFKPSLLHPNLYS*GWVCLSIL-ENKDWRPA<IMIKQIFLGIRELLNEPNTQTPAQAEAYMIYCQ

Parental  NRVEYEKR-VRAQAKKFAPS
          .RVEY.KR.VR.QAKKFA.S
Retrocopy DRVEYKKR<VRVQAKKFALS

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	67.03 RPM
SRP014902_testis	0.00 RPM	102.83 RPM
SRP018288_heart	0.00 RPM	23.97 RPM
SRP018288_kidney	0.00 RPM	45.02 RPM
SRP018288_liver	0.00 RPM	28.46 RPM
SRP018288_lung	0.00 RPM	79.83 RPM
SRP018856_adipose	0.00 RPM	53.21 RPM
SRP035408_brain	0.00 RPM	57.01 RPM
SRP035408_liver	0.00 RPM	26.83 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_319 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_319 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007721	1 retrocopy	retro_amel_1843,
Bos taurus	ENSBTAG00000038866	1 retrocopy	retro_btau_1470,
Canis familiaris	ENSCAFG00000031449	4 retrocopies	retro_cfam_1363, retro_cfam_1991, retro_cfam_2090, retro_cfam_541,
Callithrix jacchus	ENSCJAG00000013249	1 retrocopy	retro_cjac_2914,
Cavia porcellus	ENSCPOG00000010431	1 retrocopy	retro_cpor_156,
Equus caballus	ENSECAG00000015831	1 retrocopy	retro_ecab_350,
Felis catus	ENSFCAG00000027291	2 retrocopies	retro_fcat_1994, retro_fcat_873,
Loxodonta africana	ENSLAFG00000018318	1 retrocopy	retro_lafr_541,
Myotis lucifugus	ENSMLUG00000008229	2 retrocopies	retro_mluc_1112, retro_mluc_1327,
Macaca mulatta	ENSMMUG00000003654	1 retrocopy	retro_mmul_981,
Mustela putorius furo	ENSMPUG00000015763	1 retrocopy	retro_mputfur_1234,
Mus musculus	ENSMUSG00000015120	4 retrocopies	retro_mmus_1341, retro_mmus_1997, retro_mmus_3182, retro_mmus_3419,
Nomascus leucogenys	ENSNLEG00000008525	1 retrocopy	retro_nleu_1298,
Otolemur garnettii	ENSOGAG00000001428	4 retrocopies	retro_ogar_2367, retro_ogar_2731, retro_ogar_548, retro_ogar_641,
Rattus norvegicus	ENSRNOG00000017907	11 retrocopies	retro_rnor_1051, retro_rnor_1448, retro_rnor_1764, retro_rnor_1913, retro_rnor_2036, retro_rnor_2147, retro_rnor_2301, retro_rnor_2423, retro_rnor_2927, retro_rnor_708, retro_rnor_832,
Sarcophilus harrisii	ENSSHAG00000007034	1 retrocopy	retro_shar_218,
Sus scrofa	ENSSSCG00000021560	1 retrocopy	retro_sscr_319 ,
Ictidomys tridecemlineatus	ENSSTOG00000010233	3 retrocopies	retro_itri_1341, retro_itri_1459, retro_itri_1601,