RetrogeneDB ID: retro_sscr_385

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:147894719..147894926(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000029661
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSSSCG00000026064
• Aliases: None
• Description: LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17162]

Sequence

>retro_sscr_385
ATGGCAGCTAACGCTATGACTAACCCGTTGCAGCTGCTACCTCTAGAGCTTCTAGACAAGTGTATAGGATCAAGAATTCA
CATTGTGATGAAGAGTGATAAAGAGATTGTTGGCACGCTTCTCAGATTTGATGACTTTGTCAGTATGGTACCAGAAGATG
TCACTGAATTTGAAATCACACCAGAAAGAAGAAGAATTACTAAGATC

Alignment

ORF - retro_sscr_385 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.41 %
• Parental protein coverage: 75.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKL
          MAANA.TNP.QLLPLEL.DKCIGSRIHIVMKSDKEIVGTLL.FDDFV.MV.EDVTEFEITPE.RRITK.
Retrocopy MAANAMTNPLQLLPLELLDKCIGSRIHIVMKSDKEIVGTLLRFDDFVSMVPEDVTEFEITPERRRITKI

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	1.06 RPM
SRP014902_testis	0.00 RPM	3.82 RPM
SRP018288_heart	0.00 RPM	7.70 RPM
SRP018288_kidney	0.10 RPM	19.01 RPM
SRP018288_liver	0.00 RPM	11.03 RPM
SRP018288_lung	0.00 RPM	3.67 RPM
SRP018856_adipose	0.00 RPM	3.01 RPM
SRP035408_brain	0.00 RPM	24.36 RPM
SRP035408_liver	0.00 RPM	23.40 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_385 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_385 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Homo sapiens	ENSG00000106355	2 retrocopies	retro_hsap_3703, retro_hsap_4216,
Gorilla gorilla	ENSGGOG00000010325	2 retrocopies	retro_ggor_2504, retro_ggor_2824,
Microcebus murinus	ENSMICG00000005353	3 retrocopies	retro_mmur_1345, retro_mmur_69, retro_mmur_950,
Myotis lucifugus	ENSMLUG00000017028	1 retrocopy	retro_mluc_2439,
Oryctolagus cuniculus	ENSOCUG00000029043	5 retrocopies	retro_ocun_1284, retro_ocun_1452, retro_ocun_1513, retro_ocun_1556, retro_ocun_903,
Ochotona princeps	ENSOPRG00000002443	3 retrocopies	retro_opri_26, retro_opri_562, retro_opri_701,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Sus scrofa	ENSSSCG00000026064	1 retrocopy	retro_sscr_385 ,