RetrogeneDB ID: retro_itri_1428

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393484.1:2935105..2935832(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPN1
• Ensembl ID: ENSSTOG00000006379
• Aliases: None
• Description: GPN-loop GTPase 1 [Source:HGNC Symbol;Acc:17030]

Sequence

>retro_itri_1428
GTGGATGCAGCTGAGCCTCAGGATTTGGGGTCCCTTTGGTCCTCTGTGTTTCTATTGGCATTGGGGTATGGCGGGATCCA
GAAAAAAACACCTTTGTACAAAAGCTCACAGGACATCTGCATTGCCAAGGCTTTCAACCATATATGATTAATTTGGACCC
AGCCATTCATGAAGTTCCCTTCCCTGCCAATACAAATATTCATGACACCGTAAAGTATAAAGAAGTCATGAAACAATGTG
ATCTTGGGTTCAGTGGTGACATAGCAACTTCTCTCAATCACTTTGCTACCAGATCTTATAAAGAAATAAAATTTATTCAA
AAGGCCCAGAATGCATCTTGCTTGATACATCTGGACAGATTGAAAAAATTCACCTCCTCAGTTTCTGGGACATTCATCAT
TGAGGCCCTGGCATCCTCATTTCCAACAGTGGTCATTTATATAATGGACATCTTAAGATGTACTAACCCAGTGCCCCTCA
TCTCTAATGCACTCTATGCCTGTAGCACCTTGTATAAAACCAAACTGCCTTTCATTTTGGTCGTGAACAACACTGACATC
ATTGATCATAGCTTCACAGTGGAATGGATGCAGAATTTTGAGTCTTCCCAAGATGGCTTGAATCAAGAAACTACATATGT
CAGTAAACAGACTTGCTAAATAGGCCAGGTGTTAGATGAATTTTATAGCTCACTCAGGGTGGTGAATTCTCTGCTATTGT
GGGCTCT

Alignment

ORF - retro_itri_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.32 %
• Parental protein coverage: 63.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VAAADSGTSGTPNLPVCLLVLG-MAGSGK-TTFVQRLTGHLHRQSCPPYVINLDPAVHEVPFPANIDIRD
          V.AA.....G.....V.LL.LG.MAGS.K..TFVQ.LTGHLH.Q...PY.INLDPA.HEVPFPAN..I.D
Retrocopy VDAAEPQDLGSLWSSVFLLALG>MAGSRK>NTFVQKLTGHLHCQGFQPYMINLDPAIHEVPFPANTNIHD

Parental  TVKYKEVMKQYGLGPNGGIVTSLNLFATRFDQVMKFIEKAQNTSKYVLIDTPGQIEVFTWSASGTIITEA
          TVKYKEVMKQ..LG..G.I.TSLN.FATR.....KFI.KAQN.S.....D.......FT.S.SGT.I.EA
Retrocopy TVKYKEVMKQCDLGFSGDIATSLNHFATRSYKEIKFIQKAQNASCLIHLD---RLKKFTSSVSGTFIIEA

Parental  LASSFPTVVIYVMDTSRSTNPVTFMSNMLYACSILYKTKLPFIVVMNKTDIIDHSFAVEWMQDFEAFQDA
          LASSFPTVVIY.MD..R.TNPV...SN.LYACS.LYKTKLPFI.V.N.TDIIDHSF.VEWMQ.FE..QD.
Retrocopy LASSFPTVVIYIMDILRCTNPVPLISNALYACSTLYKTKLPFILVVNNTDIIDHSFTVEWMQNFESSQDG

Parental  LNQETTYVSNLTRSMSLVLDEFYSSLRVVG-VSAVVGT
          LNQETTYVS..T.....VLDEFYSSLRVV...SA.VG.
Retrocopy LNQETTYVSKQTC*IGQVLDEFYSSLRVVN<FSAIVGS

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_1428 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1428 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013421	1 retrocopy	retro_eeur_146,
Microcebus murinus	ENSMICG00000014941	1 retrocopy	retro_mmur_649,
Ictidomys tridecemlineatus	ENSSTOG00000006379	2 retrocopies	retro_itri_1428 , retro_itri_1718,
Tupaia belangeri	ENSTBEG00000007425	1 retrocopy	retro_tbel_3907,