RetrogeneDB ID: retro_sscr_148

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:309549502..309549748(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR3
• Ensembl ID: ENSSSCG00000009176
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 [Source:HGNC Symbol;Acc:15606]

Sequence

>retro_sscr_148
ATTGTTGTGTCAGATAGAGATGAAGTGCCTGTCATTCAAGTGGCCAAGGATAATGCTCCAAGCACCCTTTGAGATCTGGT
TTCTTATCTATTTTTGCCCTTGCAAAAGACAAAGGGAGCAAACTTGGACTTTCAACAAATAAAAGTAACATCTGTTACTA
TAACACCCACCAGGTGGTTTAATGCAATTGTTTACCTTTGGCTGTTGAGTTTGATAGGCAGCAACAATGCCAGTAGAGGA
CTAATT

Alignment

ORF - retro_sscr_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.62 %
• Parental protein coverage: 66.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IVVSDRDGVPVIKVANDNAP-EHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVV
          IVVSDRD.VPVI.VA.DNAP..H.LR.GFLS.FALA.D.GSKLGLS.NKS.ICYYNT.QVV..N.LPL.V
Retrocopy IVVSDRDEVPVIQVAKDNAP<KHPLRSGFLSIFALAKDKGSKLGLSTNKSNICYYNTHQVV*CNCLPLAV

Parental  SF-IASSNANTGLI
          .F.I.S.NA..GLI
Retrocopy EF>IGSNNASRGLI

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	9.29 RPM
SRP014902_testis	0.00 RPM	11.32 RPM
SRP018288_heart	0.00 RPM	21.79 RPM
SRP018288_kidney	0.00 RPM	60.38 RPM
SRP018288_liver	0.00 RPM	22.07 RPM
SRP018288_lung	0.00 RPM	24.54 RPM
SRP018856_adipose	0.00 RPM	12.82 RPM
SRP035408_brain	0.00 RPM	31.73 RPM
SRP035408_liver	0.00 RPM	18.49 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_148 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007923	1 retrocopy	retro_btau_578,
Canis familiaris	ENSCAFG00000029975	3 retrocopies	retro_cfam_1425, retro_cfam_692, retro_cfam_700,
Choloepus hoffmanni	ENSCHOG00000013153	7 retrocopies	retro_chof_1167, retro_chof_1236, retro_chof_1266, retro_chof_1536, retro_chof_166, retro_chof_1929, retro_chof_955,
Callithrix jacchus	ENSCJAG00000015196	4 retrocopies	retro_cjac_1149, retro_cjac_1821, retro_cjac_2581, retro_cjac_2786,
Cavia porcellus	ENSCPOG00000013304	2 retrocopies	retro_cpor_112, retro_cpor_208,
Echinops telfairi	ENSETEG00000009065	6 retrocopies	retro_etel_1271, retro_etel_1421, retro_etel_1621, retro_etel_1639, retro_etel_471, retro_etel_794,
Homo sapiens	ENSG00000109270	2 retrocopies	retro_hsap_1190, retro_hsap_3374,
Gorilla gorilla	ENSGGOG00000001132	2 retrocopies	retro_ggor_2283, retro_ggor_928,
Monodelphis domestica	ENSMODG00000020688	3 retrocopies	retro_mdom_1133, retro_mdom_455, retro_mdom_907,
Mustela putorius furo	ENSMPUG00000009569	2 retrocopies	retro_mputfur_590, retro_mputfur_877,
Mus musculus	ENSMUSG00000091512	1 retrocopy	retro_mmus_167,
Nomascus leucogenys	ENSNLEG00000013684	2 retrocopies	retro_nleu_1936, retro_nleu_965,
Otolemur garnettii	ENSOGAG00000005336	4 retrocopies	retro_ogar_2081, retro_ogar_2120, retro_ogar_3435, retro_ogar_451,
Pongo abelii	ENSPPYG00000014955	3 retrocopies	retro_pabe_1268, retro_pabe_2772, retro_pabe_991,
Pan troglodytes	ENSPTRG00000016310	1 retrocopy	retro_ptro_2294,
Pteropus vampyrus	ENSPVAG00000017674	1 retrocopy	retro_pvam_1378,
Rattus norvegicus	ENSRNOG00000010552	1 retrocopy	retro_rnor_2341,
Sus scrofa	ENSSSCG00000009176	1 retrocopy	retro_sscr_148 ,
Tupaia belangeri	ENSTBEG00000003682	6 retrocopies	retro_tbel_1932, retro_tbel_2172, retro_tbel_230, retro_tbel_3358, retro_tbel_4521, retro_tbel_924,
Tursiops truncatus	ENSTTRG00000015015	1 retrocopy	retro_ttru_809,