RetrogeneDB ID: retro_sscr_1208

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:85310412..85310921(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000031055
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSSSCG00000027689
• Aliases: None
• Description: spermidine synthase [Source:HGNC Symbol;Acc:11296]

Sequence

>retro_sscr_1208
AGGATGTCATTCAAGTCTCTGCCGGGCATGGCCGTTGGCTATTTGAACTCAAAGATGACCCTACTTGTGGGTGATGGTTT
TGCGTTCATGAAACAGAACTGGGATGTTTTCGATGGCATTGTCACTGACTCCTCAGACCCCCTGGGCCCTGCTGAGAGTA
TCTTCAAGGAATCCTATTATCGGCTCATGAAGACAGCACTTAAGAAGGATGGCACCCTCTGCTGCTAGGGCTAGTGTCAG
TGGCTGCACCTGAACCTCATCAAGGAGATGGGACAGTTCTGCGAATCATTGTTCCTGGCGGTGGGCTATGCTTACTGCAC
CATCACCCCCTACCCCAGTGGCCAAATTGGCTTCATGCTGTGCAGCAAAATCCAAGCACCAACTTCCCCAAGCCTGTGCA
GCAGCTGACACAGAAGCATGTGGTACAGATGCCACTGAAATTCTACAAAAATGACTTGCACCAGGCAGCCTTTGTCCTGC
CCTATTTTGCCTACAAGGCCCTGAATGAT

Alignment

ORF - retro_sscr_1208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.1 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVSKKFLPGMAVSYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEE
          ..S.K.LPGMAV.Y..SK.TL.VGDGF.FMKQN.D.FD.I.TDSSDP.GPAES.FKESYY.LMKTALK..
Retrocopy RMSFKSLPGMAVGYLNSKMTLLVGDGFAFMKQNWDVFDGIVTDSSDPLGPAESIFKESYYRLMKTALKKD

Parental  GILCCQGECQWLHLDLIKEMRQFCKSLFPVVDYAYCTIPTYPSGQIGFMLCSK-NPSTNFREPVQLLTQK
          G.LCC.G.CQWLHL.LIKEM.QFC.SLF..V.YAYCTI..YPSGQIGFMLCSK.NPSTNF..PVQ.LTQK
Retrocopy GTLCC*G*CQWLHLNLIKEMGQFCESLFLAVGYAYCTITPYPSGQIGFMLCSK<NPSTNFPKPVQQLTQK

Parental  QVEQRQLRYYNSDVHRAAFVLPEFARKALND
          .V.Q..L..Y..D.H.AAFVLP.FA.KALND
Retrocopy HVVQMPLKFYKNDLHQAAFVLPYFAYKALND

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	19.64 RPM
SRP014902_testis	0.00 RPM	40.74 RPM
SRP018288_heart	0.00 RPM	8.83 RPM
SRP018288_kidney	0.00 RPM	16.84 RPM
SRP018288_liver	0.00 RPM	32.14 RPM
SRP018288_lung	0.00 RPM	13.64 RPM
SRP018856_adipose	0.00 RPM	26.15 RPM
SRP035408_brain	0.00 RPM	57.11 RPM
SRP035408_liver	0.00 RPM	39.75 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1208 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1208 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Myotis lucifugus	ENSMLUG00000017585	1 retrocopy	retro_mluc_2458,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Mustela putorius furo	ENSMPUG00000016435	1 retrocopy	retro_mputfur_1085,
Sus scrofa	ENSSSCG00000027689	1 retrocopy	retro_sscr_1208 ,