RetrogeneDB ID: retro_sscr_1071

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:132884103..132884656(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000023072
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSTK1
• Ensembl ID: ENSSSCG00000016466
• Aliases: None
• Description: glutathione S-transferase kappa 1 [Source:HGNC Symbol;Acc:16906]

Sequence

>retro_sscr_1071
AGCTTAAGTGCAGGGATCATGAAAGACAGCAGAAACCAGCTGCCAGCTATGCTTCCCCGCAAAGCTCTGTACTTGAAAGG
TGACATTAAGCTCCTGGGACTGCATCTCCAGGTTTCCCTCCACTTCCCGAGAGATTTCTTCTCTGTGACCCTTGAAAAAG
GAAGTTTGACAGCCATGCACTTCCTCCTCTCAGTAAAACTGGAGCACCCGGCGATGCTGGAGAAAGTGTCCGGGGAACAG
AGGATGCACATCTGGTCACGGGACGAAGACATCACAGAGCCCCAGAGCATCCTGTCCACAGCAGAGAAGGCTGGCATGTC
CACAGGACAGGCCCAGGACTTCTGGAAAGGGTCTCAACACCACAGGTGAAGAACCAGCTCAAGGAGACCACTGGGGCAGC
CTGCAGACCTGGGGTCTTTGGGCTGCCCATCCCTGTGACCCACCTGTATGACAGAACCCACATGCTGTCTGGCTCTGACC
CGATGGAGTTGCTGGCACACCTGCTGGAAGAGAAGTGGATGGCCCTGTGCCTCCATCTGTAAATGCCAGACTT

Alignment

ORF - retro_sscr_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.01 %
• Parental protein coverage: 81.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLIAGILKDSGNQPPAMLPRKAVYMKEDIKRLGHHLQVPIHFPKDFFSTILGKGSLTAMRFLTTVKLEHP
          SL.AGI.KDS.NQ.PAMLPRKA.Y.K.DIK.LG.HLQV..HFP.DFFS..L.KGSLTAM.FL..VKLEHP
Retrocopy SLSAGIMKDSRNQLPAMLPRKALYLKGDIKLLGLHLQVSLHFPRDFFSVTLEKGSLTAMHFLLSVKLEHP

Parental  EMLEKVSRELWMRVWSRDEDITEPQSVLAAAEKAGMSTGQAR-GLLERVSTPEVKNQLKETTEAACKYGA
          .MLEKVS.E..M..WSRDEDITEPQS.L..AEKAGMSTGQA..GLLERVSTP.VKNQLKETT.AAC..G.
Retrocopy AMLEKVSGEQRMHIWSRDEDITEPQSILSTAEKAGMSTGQAQ<GLLERVSTPQVKNQLKETTGAACRPGV

Parental  FGLPITVAHLDDKTHMLFGSDRMELLAHLLGEKWM-GPVPPAVNARL
          FGLPI.V.HL.D.THML.GSD.MELLAHLL.EKWM.GPVPP.VNARL
Retrocopy FGLPIPVTHLYDRTHMLSGSDPMELLAHLLEEKWM<GPVPPSVNARL

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	21.64 RPM
SRP014902_testis	0.00 RPM	47.38 RPM
SRP018288_heart	0.00 RPM	29.44 RPM
SRP018288_kidney	0.00 RPM	76.44 RPM
SRP018288_liver	0.00 RPM	214.28 RPM
SRP018288_lung	0.10 RPM	28.10 RPM
SRP018856_adipose	0.14 RPM	119.29 RPM
SRP035408_brain	0.00 RPM	5.88 RPM
SRP035408_liver	0.03 RPM	122.30 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1071 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1071 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1071 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000007274	1 retrocopy	retro_fcat_807,
Mustela putorius furo	ENSMPUG00000000713	1 retrocopy	retro_mputfur_1401,
Mus musculus	ENSMUSG00000029864	1 retrocopy	retro_mmus_1859,
Rattus norvegicus	ENSRNOG00000016484	1 retrocopy	retro_rnor_1598,
Sus scrofa	ENSSSCG00000016466	1 retrocopy	retro_sscr_1071 ,