RetrogeneDB ID: retro_sscr_318

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:43190621..43191197(+)
• Located in intron of: ENSSSCG00000020990

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSSSCG00000006556
• Aliases: None
• Description: Sus scrofa tropomyosin 3 (TPM3), mRNA. [Source:RefSeq mRNA;Acc:NM_001001632]

Sequence

>retro_sscr_318
CAGCTGGCTGAAGAGGAGCTGGACTTTGCTCAAGAGCGCCTGGCCACTGCTCTGCAAAAGCTGGAAGAAGCAGAGAAAGC
TGCTGACGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACTGAGCCTTAAAAGATGAGGAAAAAATGGAAGTACAGGAAA
TCCAACTCAAAGAAGCTAAGTACATTGCAGAAGAGGCCAATAGGAAGTATAAAGAGGTGGCTTGTAAGTTGATGATTATT
TCAGGAGATTTGGAATGCACACAGGAGCAAGCTGAGCTGGCAGAGTCCCATTGCTGAGAGATGAATGAGCAGGTCAGACT
GATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATATGAGGAAGAGATAG
AGATCCTTACTGATAAACTCAAGGAGGCAGAGACCCGTGCTGAGTTTGCTAAGAGATCAGTAGCCAAGCTGGAAAAGACA
ATTGATGATTTGGAAGGTAAACTGAAATGCACCAAAGAGCAACACGTCTGTACACAAAGGATGCTGGACCGGACTCTTCT
TGACCTAAATGAGATG

Alignment

ORF - retro_sscr_318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.02 %
• Parental protein coverage: 77.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKY
          QL.EEELD.AQERLATALQKLEEAEKAADESERGMKVIEN.ALKDEEKME.QEIQLKEAK.IAEEA.RKY
Retrocopy QLAEEELDFAQERLATALQKLEEAEKAADESERGMKVIEN*ALKDEEKMEVQEIQLKEAKYIAEEANRKY

Parental  EEVARKLVIIEGDLERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKL
          .EVA.KL.II.GDLE.T.E.AELAES.C.EM.EQ.RLMDQNLKCLSAAEEKYSQKEDKYEEEI.ILTDKL
Retrocopy KEVACKLMIISGDLECTQEQAELAESHC*EMNEQVRLMDQNLKCLSAAEEKYSQKEDKYEEEIEILTDKL

Parental  KEAETRAEFAERSVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          KEAETRAEFA.RSVAKLEKTIDDLE.KLKCTKE.H.CTQRMLD.TLLDLNEM
Retrocopy KEAETRAEFAKRSVAKLEKTIDDLEGKLKCTKEQHVCTQRMLDRTLLDLNEM

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	213.70 RPM
SRP014902_testis	0.00 RPM	111.18 RPM
SRP018288_heart	0.00 RPM	41.78 RPM
SRP018288_kidney	0.00 RPM	134.07 RPM
SRP018288_liver	0.00 RPM	67.00 RPM
SRP018288_lung	0.00 RPM	401.40 RPM
SRP018856_adipose	0.00 RPM	186.50 RPM
SRP035408_brain	0.00 RPM	330.82 RPM
SRP035408_liver	0.03 RPM	226.66 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_318 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_318 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_318 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318 , retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,