RetrogeneDB ID: retro_sscr_667

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:57277744..57278139(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000023391
• Aliases: None
• Description: None

Sequence

>retro_sscr_667
CTGCAGAATAGCATCCTGGACCTCATTTCCAAAATGACCAACATGGATAGCAATAATCAGGGCCCACCAGCATTGCACAG
GATTGGAACAACTGCACTGACAGTTCAGGTTTTGTCAGGTTTTGGTGGGCTCCTCACTCTACATACCTTTGCTACTTTCA
GATCATACAGGTTTTTCAAGAGAAGTCATATCTTGTTGAAATGGAACTGTTGAAACAGCTTGAGAAATTTTCAACATCTG
TAAAACTAGAAAGGAGTTAGGATAAGAAGAGTTTTACAAATACAGACTACAATTTTACGAAATGTTTGGATATGTGTTTC
CCTGTGGTTGCTAAGTCAAGATGTCTTTTAGATAGTCTTCCAATAGCTCTACCAGACATTCTGACATCAATTATC

Alignment

ORF - retro_sscr_667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.24 %
• Parental protein coverage: 63.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQSTILGVIPNTPDPASDAQDLPPLHRIGTAALAVQVVGS-NWPKPHYTLLITGLCRFQIVQVVKEKPYP
          LQ..IL..I.......S..Q..P.LHRIGT.AL.VQV.....W..PH.T.L....C.FQI.QV..EK.Y.
Retrocopy LQNSILDLISKMTNMDSNNQGPPALHRIGTTALTVQVLSG<FWWAPHSTYL----CYFQIIQVFQEKSY-

Parental  VAEVEQLDRLEEFP-NTCKTREELGELSEQFYKYAVQLVEM-LDMSVPAVAKLRRLLDSLPREALPDILT
          ..E.E.L..LE.F..N.CKTR.ELG...E.FYKY..Q..EM.LDM..P.VAK.R.LLDSLP..ALPDILT
Retrocopy LVEMELLKQLEKFS<NICKTRKELG--*EEFYKYRLQFYEM>LDMCFPVVAKSRCLLDSLP-IALPDILT

Parental  SII
          SII
Retrocopy SII

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	18.85 RPM
SRP014902_testis	0.00 RPM	16.83 RPM
SRP018288_heart	0.00 RPM	12.26 RPM
SRP018288_kidney	0.00 RPM	24.33 RPM
SRP018288_liver	0.00 RPM	57.57 RPM
SRP018288_lung	0.00 RPM	25.05 RPM
SRP018856_adipose	0.00 RPM	24.17 RPM
SRP035408_brain	0.00 RPM	4.80 RPM
SRP035408_liver	0.00 RPM	26.57 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_667 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_667 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000023391	1 retrocopy	retro_sscr_667 ,