RetrogeneDB ID: retro_sscr_850

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:115992720..115993114(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000000359
• Aliases: None
• Description: None

Sequence

>retro_sscr_850
GGAGGGGGCCAGGCCCAGCCTACTGCAACCATGCTGTCCTGCCAGCTGAAAGAACACCAGGGCAAGCAGAATGAACTCAA
GGACCTACAGGAGAGGAAGAGGAGACAGGCTAGCGACCTGCCTGGCAGAAGTTTTGGTGGATCACCTCAACATGGGCATG
GCCCAGGCCTACATGAATTAGAAAAAGCTGGTCAATGAGGTGAAGACCCTCCAAGTCCAGGCTGCCCAGTTGGCCAAGCA
GACAGGCTAGTGAAGCCAGTGGATCTGGATGGTGGAGAACTTCAACCAGGCACTCAAGGAAATAAGGGATGTGGATAACC
GGTCTCAGAGCATCGAGCTGGACATGCACACAATTGCCACTGCTCTGGAGTATGTCTACAAAGGGAAGCTGCAG

Alignment

ORF - retro_sscr_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 86.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAPYPQPTATMLSRLLKEHQAKQNERKELQEKRRREAITA-ATCLTEALVDHLNVGVAQAYMNQRKLDHE
          G....QPTATMLS..LKEHQ.KQN...EL.....R....A.ATCL.E.LVDHLN.G.AQAYMN..KL..E
Retrocopy GGGQAQPTATMLSCQLKEHQGKQN---ELKDLQERKRRQA>ATCLAEVLVDHLNMGMAQAYMN*KKLVNE

Parental  VKTLQVQAAQFAKQTG---QWIGMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYKGQLQ
          VKTLQVQAAQ.AKQTG...QWI.MVENFNQALKEI.DV.N...SIELDM.TIATALEYVYKG.LQ
Retrocopy VKTLQVQAAQLAKQTG**SQWIWMVENFNQALKEIRDVDNRSQSIELDMHTIATALEYVYKGKLQ

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	61.99 RPM
SRP014902_testis	0.00 RPM	65.35 RPM
SRP018288_heart	0.00 RPM	50.32 RPM
SRP018288_kidney	0.00 RPM	40.49 RPM
SRP018288_liver	0.00 RPM	16.15 RPM
SRP018288_lung	0.00 RPM	24.74 RPM
SRP018856_adipose	0.00 RPM	62.24 RPM
SRP035408_brain	0.00 RPM	54.02 RPM
SRP035408_liver	0.00 RPM	18.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_850 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_850 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Cavia porcellus	ENSCPOG00000001818	2 retrocopies	retro_cpor_1260, retro_cpor_846,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023,
Pteropus vampyrus	ENSPVAG00000017748	1 retrocopy	retro_pvam_121,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850 ,
Ictidomys tridecemlineatus	ENSSTOG00000010338	1 retrocopy	retro_itri_467,