RetrogeneDB ID: retro_sscr_1069

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:118345201..118345939(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000022995
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000008277
• Aliases: None
• Description: None

Sequence

>retro_sscr_1069
ATGAGGCTTCGGAACCAGCTCGTCAGTGCACAAGACGGACCCGCTACAGAACTAGGAGGAGGTTCGAGTAAAGATCAAAG
ACTTGAATGAGCACAGGTCTGCTGCCTGTGCGCAGGCTACTTCGTGGATGCCACTACCATCACTGAGTGTCTTCATATGT
TCTGCAAGAGTTGTATTGTGAAGTACCTCCAAACCAGCAAGTACTGCCCCATGTGCAACATCAAGATCCATGAGACACAG
CCACTGCTCAACCTCAAACTTGACCAGGTCATGCAGGACATCGTGTACAAGCTAGTGCCAGGCTTGCAAGACAATGAAGA
GAAACGGATCCGAGAATTCTACCAGTCCCGAGACTTGGACAGGATCACCCAGCCCAGTGGGGAAGAGCCAGCCCTGAGCA
ACCTCGGCCTCCCCTTCAGCAGTTTCGACCACTCAAAAGCCCACTACCATCACTATGATGAGCAGCTAAGCCTATGCCTG
GAGAAGCTGAGTTCTAGCAAAGACAAGAATAAAAGCGTCCTGCAGAACAAATATGTCCGATGTTCTGTTAGAGCTGAGGT
TCGCTATTTCCAGAAGGTCATCTGTCACCGCTTGATGCTAAGTCCCCAGCATGTGCAGCTCCTTTTTGACAATGAAGTTC
TCCCTGATCACATGACCATGAAGCAGATATGGCTCTCCCGCTGGTTCGGCAAGCCATCCCCTTTGCTTTTACAATACAGT
GTGAAAGAGAAGAGGAGG

Alignment

ORF - retro_sscr_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 95.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRLRNQLQSVY-KMDRYGTR-EEVRVKIKDLNEHI-VCCLCAGYFVDATTITECLHTFCKSCIVKYLQTS
          MRLRNQL.S......RY.TR.EEVRVKIKDLNEH..VCCLCAGYFVDATTITECLH.FCKSCIVKYLQTS
Retrocopy MRLRNQLVSAQ<RRTRYRTR<EEVRVKIKDLNEHR<VCCLCAGYFVDATTITECLHMFCKSCIVKYLQTS

Parental  KYCPMCNIKIHETQPLLNLKLDRVMQDIVYKLVPGLQDSEEKRIREFYQSRGLDRITQPSGEEPALSNLG
          KYCPMCNIKIHETQPLLNLKLD.VMQDIVYKLVPGLQD.EEKRIREFYQSR.LDRITQPSGEEPALSNLG
Retrocopy KYCPMCNIKIHETQPLLNLKLDQVMQDIVYKLVPGLQDNEEKRIREFYQSRDLDRITQPSGEEPALSNLG

Parental  LPFSSFDHSKAHYYRYDEQLSLCLERLSSGKDKNKSVLQNKYVRCSVRAEVRHLRKVLCHRLMLSPQHVQ
          LPFSSFDHSKAHY..YDEQLSLCLE.LSS.KDKNKSVLQNKYVRCSVRAEVR...KV.CHRLMLSPQHVQ
Retrocopy LPFSSFDHSKAHYHHYDEQLSLCLEKLSSSKDKNKSVLQNKYVRCSVRAEVRYFQKVICHRLMLSPQHVQ

Parental  LLFDNEVLPDHMTMKQIWLSRWFGKPSPLLLQYSVKEKRR
          LLFDNEVLPDHMTMKQIWLSRWFGKPSPLLLQYSVKEKRR
Retrocopy LLFDNEVLPDHMTMKQIWLSRWFGKPSPLLLQYSVKEKRR

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	1.46 RPM
SRP014902_testis	0.00 RPM	1.56 RPM
SRP018288_heart	0.00 RPM	0.89 RPM
SRP018288_kidney	0.00 RPM	2.56 RPM
SRP018288_liver	0.16 RPM	2.88 RPM
SRP018288_lung	0.10 RPM	5.19 RPM
SRP018856_adipose	0.11 RPM	4.36 RPM
SRP035408_brain	0.03 RPM	1.91 RPM
SRP035408_liver	0.00 RPM	0.88 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1069 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115289	1 retrocopy	retro_hsap_1029,
Mus musculus	ENSMUSG00000069678	1 retrocopy	retro_mmus_2722,
Nomascus leucogenys	ENSNLEG00000000752	1 retrocopy	retro_nleu_907,
Pongo abelii	ENSPPYG00000012270	1 retrocopy	retro_pabe_862,
Pan troglodytes	ENSPTRG00000012094	1 retrocopy	retro_ptro_704,
Sorex araneus	ENSSARG00000007319	1 retrocopy	retro_sara_448,
Sus scrofa	ENSSSCG00000008277	1 retrocopy	retro_sscr_1069 ,