RetrogeneDB ID: retro_sscr_1169

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:88388658..88389111(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000024086
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1169
ATGTGTGTTCTGAGAGACCAGCAGCATTGTGATGAGGCCAAGGCTGTGGATATCCCGCACATGGACATCAAGGCAATGAA
GAAACTCAACAAGAATAAGAAACTGGTCAAGAATCTGGCCAAGAAGTGTGATGCCTCTTTTGCTTTGGAGTCTCTAATCA
AACAGATTCCACTAATCCTGGGCCCTGGCCTGAATAAGGCTGGCAAGTTCCCTTCCTTGCTGACCCACAATGAGAATATT
GTGGCTAGAGTTGATGAAGTCCACAATCAAGTTCCAGATGAAGAAGGTGCTGTGTCTAGCAGTGGCTGTTGTCCAGGTGA
AGATGGCAGATGATGAGCTTGTGTACAACATCCACTTAGCTGTCAACTTCCTGGTGTCATTGCTCAAGAAAAAATGACAG
AACATCTGGGCTTTTACATTAAGAGCACCATGAGCAAGCCCCAGCACCTATAC

Alignment

ORF - retro_sscr_1169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 86.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VCVLGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKF
          .CVL.DQQHCDEAKAVDIPHMDI.A.KKLNKNKKLVK.LAKK.DA..A.ESLIKQIP.ILGPGLNKAGKF
Retrocopy MCVLRDQQHCDEAKAVDIPHMDIKAMKKLNKNKKLVKNLAKKCDASFALESLIKQIPLILGPGLNKAGKF

Parental  PSLLTHNENMVAKVDEVKSTIKFQMKKV-LCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRA
          PSLLTHNEN.VA.VDEV..........V.L..AV....VKM.DDELVYNIHLAVNFLVSLLKK..QN..A
Retrocopy PSLLTHNENIVARVDEVHNQVPDEEGAV>LAVAVV--QVKMADDELVYNIHLAVNFLVSLLKKK*QNIWA

Parental  -LYIKSTMGKPQRLY
          ..YIKSTM.KPQ.LY
Retrocopy <FYIKSTMSKPQHLY

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	0.13 RPM	412.66 RPM
SRP014902_testis	0.28 RPM	595.91 RPM
SRP018288_heart	0.00 RPM	480.18 RPM
SRP018288_kidney	0.10 RPM	296.50 RPM
SRP018288_liver	0.00 RPM	235.55 RPM
SRP018288_lung	0.00 RPM	299.98 RPM
SRP018856_adipose	0.00 RPM	773.63 RPM
SRP035408_brain	0.00 RPM	256.82 RPM
SRP035408_liver	0.00 RPM	287.98 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1169 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1169 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,