RetrogeneDB ID: retro_sscr_871

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:55975081..55975766(-)
• Located in intron of: ENSSSCG00000003322

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A36
• Ensembl ID: ENSSSCG00000011669
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier ), member 36 [Source:HGNC Symbol;Acc:25554]

Sequence

>retro_sscr_871
TTCTCTGGCCAGAGGAACCTGACAGTGCATCTGCTTGTAAGGGAATGTAGTGGTATAGGAGGGCTATTACAACTGGAAGT
TGTAATAATTCAGCCTTGGCCTTCTGCTGTGATGCTTTCTGGCTCTGAAGTTTAGCTGAACACCATGGCTAGAGCTAATG
TCAATTGGACCGTATTCCTTGGATCTTTCCTTTGCCTAACAGTGACCTTAGTAAAGGAGGGCCTTGCTCCTTATTTAGAA
GATCAGGCCTGAATTTAATGGGGTAGCATCTTCCAGAGCAACATTCTTTGCTGGTTATTCAAATTGCAAGGAAAAGGCTG
AATGGTGTATTTGATCTTGATTTTACCTGGTACATGATTTCGATTACAGTGGCCTATTTTACCGTAATCACAGAAATCAG
TCCCATTTGGCTAAAAAGAATTTGTTGCAGCTTCATGCAAGGAACTATGGGGAAAAGTGAATGAGAGCTCTTGAATGTGG
TCGTCAAGTATATTAGAAGGCCAAAGAAGGTTTTATAAGGGCATGTCTGCTTCCTCTGGTGGCATATCAGAGACTCCTAT
TCATTGGTTATTTGTGAAATTATTAGGCAAAAACTACTGGAGTAAAAGATTACTTTGACAATGGCAGATAATGAAAATCT
GTAAAAGAAGTATCAGATTTTGGGGGAATGATGCTGCTGTCATCT

Alignment

ORF - retro_sscr_871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.96 %
• Parental protein coverage: 75.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  FAKSQLLTHFIALHRCGGTVGAILTCPLEVVKTRLQSSSVTLYISEVHLNTMAGASVNRVVSPGPLHCLK
          F.....LT.......C.G..G..L...LEVV......S.V.L..SEV.LNTMA.A.VN..V..G...CL.
Retrocopy FSGQRNLTVHLLVRECSG-IGGLLQ--LEVVIIQPWPSAVMLSGSEV*LNTMARANVNWTVFLGSFLCLT

Parental  VILEKE-GPRSLFRGLGPNLV-GVAPSRAIYFAAYSNCKEK-LNGLFDPDSTQVHMISAAMAGFTAITAT
          V.L.KE.GP.SLFR..G.NL..GVA.SRA..FA.YSNCKEK.LNG.FD.D.T...MIS...A.FT.IT..
Retrocopy VTLVKE<GPCSLFRRSGLNLM<GVASSRATFFAGYSNCKEK>LNGVFDLDFTW-YMISITVAYFTVITEI

Parental  NPIWL-IKTRLQLDARNRGEKRMGAFECVRKVYQTDGLRGFYR-GMSASYAGISETVIHF-VIYESIKQK
          .PIWL..K..LQL.ARN.GEK.M.A.EC.R.VY......GF.R.GMSAS..GISET.IH..VI.E.I.QK
Retrocopy SPIWL<KKNLLQLHARNYGEK*MRALECGRQVY-*KAKEGFIR<GMSASSGGISETPIHW<VICEIIRQK

Parental  LLEYKIASTMETEE-ESVKEASDFVGMMLAAA
          LLE.KI..TM...E..SVKE.SDF.GMML...
Retrocopy LLE*KITLTMADNE<KSVKEVSDFGGMMLLSS

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	8.89 RPM
SRP014902_testis	0.14 RPM	19.38 RPM
SRP018288_heart	0.13 RPM	19.04 RPM
SRP018288_kidney	0.20 RPM	32.51 RPM
SRP018288_liver	0.00 RPM	3.20 RPM
SRP018288_lung	0.41 RPM	21.79 RPM
SRP018856_adipose	0.00 RPM	25.19 RPM
SRP035408_brain	0.06 RPM	2.95 RPM
SRP035408_liver	0.00 RPM	1.09 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_871 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_871 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871 ,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146, retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603,