RetrogeneDB ID: retro_sscr_474

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:129865407..129865647(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSSSCG00000009036
• Aliases: None
• Description: LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17017]

Sequence

>retro_sscr_474
ATGAGTATGAAGAAGCAAACACCCAGTGACTTCCTCAAGAAAATCACTGGACAACCAGTAGTGGTAAAATTAAATTCTGG
AATGGATTACTGACGGACCCTGGTTTTCCTGGATGGCTACATGAATGTTGCCTTGGAACAGATGGAGGAGTATGTAAACG
GAGAACTGAAGAATAAGTATGGGGGTGCATTTATCCGAGGGAACAATGTGTTGTGCATAAGTACACAGAAGAGGAGCATG

Alignment

ORF - retro_sscr_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNV
          MS..KQTPSDFLK.I.G.PVVVKLNSG.DY...L..LDGYMN.ALEQ.EEYVNG.LKNKYG.AFIRGNNV
Retrocopy MSMKKQTPSDFLKKITGQPVVVKLNSGMDY*RTLVFLDGYMNVALEQMEEYVNGELKNKYGGAFIRGNNV

Parental  LYISTQKRRM
          L.ISTQKR.M
Retrocopy LCISTQKRSM

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	2.39 RPM
SRP014902_testis	0.00 RPM	23.90 RPM
SRP018288_heart	0.00 RPM	15.35 RPM
SRP018288_kidney	0.00 RPM	14.87 RPM
SRP018288_liver	0.00 RPM	14.23 RPM
SRP018288_lung	0.00 RPM	23.93 RPM
SRP018856_adipose	0.00 RPM	16.16 RPM
SRP035408_brain	0.00 RPM	13.66 RPM
SRP035408_liver	0.00 RPM	24.25 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_474 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474 , retro_sscr_475,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,