RetrogeneDB ID: retro_sscr_410

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:31203530..31204095(+)
• Located in intron of: ENSSSCG00000009778

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPR
• Ensembl ID: ENSSSCG00000008309
• Aliases: None
• Description: sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) [Source:HGNC Symbol;Acc:11257]

Sequence

>retro_sscr_410
GGAAGCTGGAGGCCCAGCTGGGCTCCAGGCGGCCTGGCCACCGACCTGGGCCCTGAGGCCCGCTTGCAGCAGTTGCTTGG
CACCCTGCACAAGCTCCCCAGGCCCAAGGGCCTGCAGCAAGTGCTGCTCATCAAAAGTGCAGCCACTCTTGGGGATGTGT
CCAGAGGCTTCGTGGATCTGGCTGACCCAGCTGAAGTGAACAGCTGCTGGGCTCTGAACTTGACATCCATGCTCTTCCTG
ACCTCCAGTTCCTGAAGGCTTTCCCAGCCAGTCCTGGCCTTGGCAGTAATGTGGTTAACATCAATTGTGCCCTGGAGCCC
TTCAGAGACTGGGCACTGTACTGTTTAGGAAAGGCTGCCCATGACATGATGTTTCCGGTCCTGGCTGCAGAGGGCCCTAG
TGTGATAGTGCTGAGCTACACCCCGGTTTCCCGGACACAGACCTGCAGCTGTTAGCCCAGGAGACGTCCATGGACCCAGA
CTTGTGAAAAATGCTGCAGGAGCTGAAGAGAAAGGGGGAACTTGTGAATCTCAAGGTATCAGCCCAGAAACTGCTAAACT
TGCTG

Alignment

ORF - retro_sscr_410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 71.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSERPDLRVVRVPADLGAEAGLQQLLGALRELPRPEGLQRVLLFNNAASLGDVSKSFVDLTDSAEVNSYW
          GS.RP.........DLG.EA.LQQLLG.L..LPRP.GLQ.VLL...AA.LGDVS..FVDL.D.AEVNS.W
Retrocopy GSWRPSWAPGGLATDLGPEARLQQLLGTLHKLPRPKGLQQVLLIKSAATLGDVSRGFVDLADPAEVNSCW

Parental  ALNLTSMLCLTSS-FLKAFPDSPGLSRMVVNISSICAVKPFKGWALYCAGKAARDMIYQVLAAEDPSLRV
          ALNLTSML.LTSS.FLKAFP.SPGL...VVNI...CA..PF..WALYC.GKAA.DM...VLAAE.PS..V
Retrocopy ALNLTSMLFLTSS<FLKAFPASPGLGSNVVNIN--CALEPFRDWALYCLGKAAHDMMFPVLAAEGPSVIV

Parental  LSYA-PGPLDTDMQQIAREASVDPDLRKRLQELKRKGELVDCKVSAQKLLNLL
          LSY..PG..DTD.Q..A.E.S.DPDL.K.LQELKRKGELV..KVSAQKLLNLL
Retrocopy LSYT<PGFPDTDLQLLAQETSMDPDL*KMLQELKRKGELVNLKVSAQKLLNLL

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	1.99 RPM
SRP014902_testis	0.14 RPM	46.82 RPM
SRP018288_heart	0.03 RPM	20.25 RPM
SRP018288_kidney	0.00 RPM	36.25 RPM
SRP018288_liver	0.00 RPM	41.42 RPM
SRP018288_lung	0.00 RPM	26.58 RPM
SRP018856_adipose	0.02 RPM	76.65 RPM
SRP035408_brain	0.00 RPM	17.28 RPM
SRP035408_liver	0.00 RPM	23.19 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_410 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_410 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_410 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000012959	1 retrocopy	retro_ogar_2301,
Pelodiscus sinensis	ENSPSIG00000013998	1 retrocopy	retro_psin_10,
Pteropus vampyrus	ENSPVAG00000016383	1 retrocopy	retro_pvam_802,
Sus scrofa	ENSSSCG00000008309	1 retrocopy	retro_sscr_410 ,