RetrogeneDB ID: retro_sscr_853

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:143517388..143517919(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000003838
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GLO1
• Ensembl ID: ENSSSCG00000027778
• Aliases: None
• Description: glyoxalase I [Source:HGNC Symbol;Acc:4323]

Sequence

>retro_sscr_853
TCTGGCGGCCTTAACAACGGGGCTGCCCACAGCTGCTGCTCTGACCCACATCCCAGCACCAAGGATTTTTCTCTTGCAGC
AGGCCACGCTGCGAATTAAGGATCCTAAGAAGTCGCTGGATTTTTATACTAGAATTCTTAGAATGACGCTACTCCAAAAA
TTAGATTTTCCCACTATGACATTTTCACTCTATCTCTTGGCTTATGAGGATAAAAATGACATCCCAAAAGATAAAGACGA
AAAAGTAGCGTGGGCATTCTCCAGAAAAGCTATGCTTGGACTGACACACAACTGGGGCACTGAAGATGATGCCAGCCAGA
GTTACCACAGTGGCAATTCAGACCCTTGGGAATTTGGTCCCATTGGAACTGCTCTTCCTGACGTTCATGGTGCTTGTAGA
AGATGTGAAGAACTAGGAGCCAAATTTGTGAAGAAACCTGATGATGGTAAATGAAAGCCTTGGCATTTATTCCAGATCCT
GATGGCTACTGGATTGAAATTTTGAATCCTAGCAAAATGACAACTATTATT

Alignment

ORF - retro_sscr_853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.56 %
• Parental protein coverage: 96.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSGLTDEAALACCSDPDPSTKDF-LFQQTMLRIKDPKKSLDFYTRILGMTLLQKLDFPTMKFSLYFLAYE
          S.GL...AA..CCSDP.PSTKDF.L.QQ..LRIKDPKKSLDFYTRIL.MTLLQKLDFPTM.FSLY.LAYE
Retrocopy SGGLNNGAAHSCCSDPHPSTKDF>LLQQATLRIKDPKKSLDFYTRILRMTLLQKLDFPTMTFSLYLLAYE

Parental  DKNDIPKDKSEKAAWAFSRKATLELTHNWGTEDDESQSYHSGNSDPRGFGHIGIAVPDVHGACKRFEELG
          DKNDIPKDK.EK.AWAFSRKA.L.LTHNWGTEDD.SQSYHSGNSDP..FG.IG.A.PDVHGAC.R.EELG
Retrocopy DKNDIPKDKDEKVAWAFSRKAMLGLTHNWGTEDDASQSYHSGNSDPWEFGPIGTALPDVHGACRRCEELG

Parental  VKFVKKPDDGK-MKGLAFIQDPDGYWIEILNPNNMITII
          .KFVKKPDDGK.MK.LAFI.DPDGYWIEILNP..M.TII
Retrocopy AKFVKKPDDGK<MKALAFIPDPDGYWIEILNPSKMTTII

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	38.09 RPM
SRP014902_testis	0.00 RPM	46.25 RPM
SRP018288_heart	0.05 RPM	107.08 RPM
SRP018288_kidney	0.00 RPM	271.38 RPM
SRP018288_liver	0.00 RPM	231.55 RPM
SRP018288_lung	0.00 RPM	47.76 RPM
SRP018856_adipose	0.00 RPM	81.16 RPM
SRP035408_brain	0.00 RPM	151.72 RPM
SRP035408_liver	0.00 RPM	201.56 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_853 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_853 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012703	2 retrocopies	retro_btau_1003, retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012, retro_rnor_1024,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853 ,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,