RetrogeneDB ID: retro_itri_1626

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393580.1:80168..80695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLO1
• Ensembl ID: ENSSTOG00000005821
• Aliases: None
• Description: glyoxalase I [Source:HGNC Symbol;Acc:4323]

Sequence

>retro_itri_1626
CAGCCTGAGTCTGGCCTCACTGACAAGGTCAGCCTCAGTTGCTGCTCTACCTAGATCCTAGCACCAAGGATTTTCTGTTG
TAACAGACCATGCTGAGAATTAAGAATCCTAAGAAGTCACTGGGTTTTTATACTAAAGTCCTTGGAATGACACTAATTCA
AATATTAGATTTTCCTACTATGAAATTTTCACTGTATTTCTTATCTTATGAGGATAAAAATGACCTCTTTAAAGATAAAA
ATGAAAAAATAGCATGAATATTCTCCAGAAAAGTTATACTTGAACTGACACACAGTTGGAGTGCTGAAAATGATGAGACT
CAGAGTTACCATAAGGGCAATTCAGACCTTCCCGAATTTGGTCACATTGGAATTGCTGTTTCTGATGTACGTGGAGTTTG
TAAAAGATTTGAAGAACTGGGAGTCAAATTTGTGAAGAAACCTGCTGGTGGTCAAATGAAAGGTCTGGCATTTATTCAAG
GTCCTGATGGCTACTGGATTTAAATTTTGAATGCAAACAAAATGGCG

Alignment

ORF - retro_itri_1626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.53 %
• Parental protein coverage: 97.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPATGLTDEVALSCCSD-PDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGMTLIQKLDFPTMNFSLYFLA
          QP..GLTD.V.LSCCS...DPSTKDFLL.QTMLRIK.PKKSL.FYT.VLGMTLIQ.LDFPTM.FSLYFL.
Retrocopy QPESGLTDKVSLSCCST<LDPSTKDFLL*QTMLRIKNPKKSLGFYTKVLGMTLIQILDFPTMKFSLYFLS

Parental  YEDKNDFPKDKNEKMAWVFSRKATLELTHNWGTENDETQSYHNGNSDPRGFGHIGIAVPDVYGACKRFEE
          YEDKND..KDKNEK.A..FSRK..LELTH.W..ENDETQSYH.GNSD...FGHIGIAV.DV.G.CKRFEE
Retrocopy YEDKNDLFKDKNEKIA*IFSRKVILELTHSWSAENDETQSYHKGNSDLPEFGHIGIAVSDVRGVCKRFEE

Parental  LGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIA
          LGVKFVKKP..G.MKGLAFIQ.PDGYWI.ILN.NK.A
Retrocopy LGVKFVKKPAGGQMKGLAFIQGPDGYWI*ILNANKMA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1626 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1626 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,