RetrogeneDB ID: retro_sscr_120

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:103537751..103538265(+)
• Located in intron of: ENSSSCG00000021383

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSSSCG00000001543
• Aliases: None
• Description: Sus scrofa ribosomal protein L10a (RPL10A), mRNA. [Source:RefSeq mRNA;Acc:NM_001097477]

Sequence

>retro_sscr_120
ACAGACGCTTCTCGGGCACCTCAGGCCTAAGTCTACTCCCCGCCCCAAGTTCTCCGTTTGTATTCTGGGAGACCAGCAGC
ATTGTGATGAGGCCAAGGCTGTGGATATCCCACACATGGACATCGAGGCACTGAAGAAACTCAACAAGAATAAGAAACTG
GTCAAGAAGCTGGCCAAGAAGTATGATGCCTTTTTGGCTTCAGAGTCTCTAATCAAGCAGATTCCATGAATCCTGGGCCC
TGGCCTGAATAAGGCTGGCAAGTTCCCTTCCTTGCTGACCCACAATGAGAATATGGTGGCCAAAGTTGATGAAGTGAAGT
CCACGATCAAGTTCCAGATGAAGAAGGTGCTGTGTCTCGAAGTGGCTATTGGCCACGTGAAGACGACAGATGATGAGCTT
GTGTATAACATCCTTTTTGCTGTCAACTTCCTGGTGTCATTGCTCAAGAAAAATTGGCAGAACGTCTGAGCTTTGTACAT
TAAGAGCTCCAGGGGCAAATGCCAGCACCTGTAC

Alignment

ORF - retro_sscr_120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 97.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TNASRAP-SGLSLL-PAP-FSVCVLGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLAS
          T.ASRAP.SGLSLL.P.P.FSVC.LGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLAS
Retrocopy TDASRAP<SGLSLL<PRPKFSVCILGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLAS

Parental  ESLIKQIPRILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNI
          ESLIKQIP.ILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCL.VA.GHVK.TDDELVYNI
Retrocopy ESLIKQIP*ILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLEVAIGHVKTTDDELVYNI

Parental  HLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY
          ..AVNFLVSLLKKNWQNV.ALYIKS..GK.Q.LY
Retrocopy LFAVNFLVSLLKKNWQNV*ALYIKSSRGKCQHLY

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	0.27 RPM	412.66 RPM
SRP014902_testis	0.14 RPM	595.91 RPM
SRP018288_heart	0.47 RPM	480.18 RPM
SRP018288_kidney	0.49 RPM	296.50 RPM
SRP018288_liver	0.96 RPM	235.55 RPM
SRP018288_lung	0.61 RPM	299.98 RPM
SRP018856_adipose	0.31 RPM	773.63 RPM
SRP035408_brain	0.06 RPM	256.82 RPM
SRP035408_liver	0.06 RPM	287.98 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_120 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_120 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019494	4 retrocopies	retro_btau_138, retro_btau_1501, retro_btau_1634, retro_btau_87,
Dasypus novemcinctus	ENSDNOG00000012921	3 retrocopies	retro_dnov_157, retro_dnov_1917, retro_dnov_469,
Equus caballus	ENSECAG00000014090	2 retrocopies	retro_ecab_512, retro_ecab_517,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Microcebus murinus	ENSMICG00000012458	3 retrocopies	retro_mmur_1381, retro_mmur_384, retro_mmur_93,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Mus musculus	ENSMUSG00000037805	8 retrocopies	retro_mmus_1110, retro_mmus_1304, retro_mmus_1422, retro_mmus_149, retro_mmus_1737, retro_mmus_2038, retro_mmus_2652, retro_mmus_452,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Pongo abelii	ENSPPYG00000016529	10 retrocopies	retro_pabe_1208, retro_pabe_1597, retro_pabe_2614, retro_pabe_2759, retro_pabe_3302, retro_pabe_3315, retro_pabe_3377, retro_pabe_357, retro_pabe_451, retro_pabe_475,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Sus scrofa	ENSSSCG00000001543	7 retrocopies	retro_sscr_1169, retro_sscr_1174, retro_sscr_120 , retro_sscr_246, retro_sscr_379, retro_sscr_461, retro_sscr_465,