RetrogeneDB ID: retro_sscr_1182

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:6880621..6880955(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSSSCG00000011491
• Aliases: None
• Description: THO complex 7 homolog (Drosophila) [Source:HGNC Symbol;Acc:29874]

Sequence

>retro_sscr_1182
TGTAGCATACCTGGAGAAATGAAAGAAAAATTCAATGCAGAAGGCAGATTTGTCAGGAGAAACTAGTATGGGAAAAGTAG
GGAAGAATCCAATGTTTTTACACAAATATTGTAACACCATATAAACAGGCACGAGCCATAAAAGAACTACAGGCTCTGGG
AGAAGACTTGGGACTCTTCAAACATAGTAAAGAAAATACTGAAGATAAGCTAGAACTGAGGTCCAAACACTACCATGTTC
TTTTTCAGCCCCTCATGAACTTCAGCAAAATGACGGCAAGCTCTCAGAAGTGGAAGAGGTTCAAGAAACATACATGCAAA
CCGATTGCCGGCCC

Alignment

ORF - retro_sscr_1182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.42 %
• Parental protein coverage: 56.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CSIAGA-HEKIAECKKQILQAKRI-RKNRQEYDALAKVIQHHPDRHE-TLKELEALGKELEHLSHIKESV
          CSI.G...E....C..QI.Q.K....K.R.E.........HH..RHE...KEL.ALG..L....H.KE..
Retrocopy CSIPGE<NERKIQCRRQICQEKLV>GKSREESNVFTQIL*HHINRHE<AIKELQALGEDLGLFKHSKENT

Parental  EDKLELRRKQFHVLLSTI-HELQQTLENDEKLSEVEEAQETSMETDPKP
          EDKLELR.K..HVL.....HELQQ...ND.KLSEVEE.QET.M.TD..P
Retrocopy EDKLELRSKHYHVLFQPL<HELQQ---NDGKLSEVEEVQETYMQTDCRP

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	12.21 RPM
SRP014902_testis	0.00 RPM	18.95 RPM
SRP018288_heart	0.00 RPM	72.45 RPM
SRP018288_kidney	0.00 RPM	56.35 RPM
SRP018288_liver	0.00 RPM	41.90 RPM
SRP018288_lung	0.00 RPM	29.53 RPM
SRP018856_adipose	0.00 RPM	32.54 RPM
SRP035408_brain	0.00 RPM	114.37 RPM
SRP035408_liver	0.00 RPM	52.87 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1182 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127, retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585, retro_lafr_774,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182 ,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,