RetrogeneDB ID: retro_sscr_541

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:23462810..23462991(-)
• Located in intron of: ENSSSCG00000016842

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMA7
• Ensembl ID: ENSSSCG00000011351
• Aliases: None
• Description: translation machinery associated 7 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26932]

Sequence

>retro_sscr_541
TCAGCCCGTGAAGGTGGCAAGAAGAAGCCCCTGAAGCAGTCCAAGGAAATGGACAAGGAAGATAAGGCATTCAAGAAGAA
ACAGAAGTTAGAGCAGAAGAAAATCAAGGAGCTAAAAATGAAGACCTCAGGGATATAAATACCCTCTGGCCACAGGTGGA
GTTAAGAAATCTGACAAAAAG

Alignment

ORF - retro_sscr_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.62 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGREGGKKKPLKQPKKQAKEMDEEDKAFKQKQKEEQ-KKLEELKAKAAG-KGPLATGGIKKSGKK
          S.REGGKKKPL....KQ.KEMD.EDKAFK.KQK.EQ..K....K....G.K.PLATGG.KKS.KK
Retrocopy SAREGGKKKPL----KQSKEMDKEDKAFKKKQKLEQ>RKSRS*K*RPQGYKYPLATGGVKKSDKK

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	16.33 RPM
SRP014902_testis	0.00 RPM	62.66 RPM
SRP018288_heart	0.03 RPM	81.49 RPM
SRP018288_kidney	0.00 RPM	118.21 RPM
SRP018288_liver	0.00 RPM	71.80 RPM
SRP018288_lung	0.10 RPM	12.93 RPM
SRP018856_adipose	0.00 RPM	154.81 RPM
SRP035408_brain	0.00 RPM	101.95 RPM
SRP035408_liver	0.00 RPM	62.18 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_541 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001193	6 retrocopies	retro_amel_1070, retro_amel_1643, retro_amel_270, retro_amel_503, retro_amel_826, retro_amel_879,
Callithrix jacchus	ENSCJAG00000002871	18 retrocopies	retro_cjac_1370, retro_cjac_1449, retro_cjac_1504, retro_cjac_1667, retro_cjac_1670, retro_cjac_1704, retro_cjac_1918, retro_cjac_2092, retro_cjac_2258, retro_cjac_2422, retro_cjac_2629, retro_cjac_2673, retro_cjac_2692, retro_cjac_2799, retro_cjac_3651, retro_cjac_536, retro_cjac_81, retro_cjac_849,
Felis catus	ENSFCAG00000026902	5 retrocopies	retro_fcat_138, retro_fcat_1630, retro_fcat_173, retro_fcat_57, retro_fcat_630,
Homo sapiens	ENSG00000232112	11 retrocopies	retro_hsap_131, retro_hsap_154, retro_hsap_2151, retro_hsap_2561, retro_hsap_2888, retro_hsap_2934, retro_hsap_3115, retro_hsap_3402, retro_hsap_3736, retro_hsap_3852, retro_hsap_3964,
Gorilla gorilla	ENSGGOG00000028044	3 retrocopies	retro_ggor_11, retro_ggor_2002, retro_ggor_209,
Mus musculus	ENSMUSG00000091537	11 retrocopies	retro_mmus_1216, retro_mmus_1582, retro_mmus_1632, retro_mmus_2117, retro_mmus_2189, retro_mmus_2222, retro_mmus_2545, retro_mmus_2975, retro_mmus_3235, retro_mmus_389, retro_mmus_412,
Pan troglodytes	ENSPTRG00000041769	9 retrocopies	retro_ptro_136, retro_ptro_1492, retro_ptro_150, retro_ptro_1638, retro_ptro_1953, retro_ptro_1976, retro_ptro_2312, retro_ptro_2535, retro_ptro_2691,
Rattus norvegicus	ENSRNOG00000042689	2 retrocopies	retro_rnor_316, retro_rnor_894,
Rattus norvegicus	ENSRNOG00000047225	1 retrocopy	retro_rnor_1709,
Sus scrofa	ENSSSCG00000011351	6 retrocopies	retro_sscr_133, retro_sscr_19, retro_sscr_299, retro_sscr_541 , retro_sscr_735, retro_sscr_910,