RetrogeneDB ID: retro_itri_387

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393288.1:19382539..19383010(+)
• Located in intron of: ENSSTOG00000000456

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000013420
• Aliases: None
• Description: None

Sequence

>retro_itri_387
ATGTCTGAGACCAAGAACAACCCTGAGAAAGCATCGTTCTTCTTCTCCGAGATCACCAGCGCCTCGTCAGCCATGATCTT
CAGTGCCTTGGGTGCCACCTATTGCATGCCCAAGAGTGGCACTGGCATCGCAGCTGTGTAAGTCATGAAGCCAGAGAAGA
TCATGAAGTCCATCACCCCGTGTTCATGGCTGGGCTCTTTGCCATCTATGGCCTAGTGGTGGCAGTCCTCATTGCCAACT
CCCTGAATGATGGTATGAGCCTCTACAGGAGTTTACTCCAGCTGGGTGCAGGCCAGAGTGTGGGCCTCAGCGGCCTGGCA
GGCTGGCTTTGCCATTGGCATTGTGGGGGATGCTGGTGTTCAGGGCACTGCCCAGCAGCCCTGACTGTTTGTGGGCATGA
TCCTGATCCTAATCTTCACTGAGGTGCTTGGCCTCTAAGGTCTCATCATGGCCCTCATACTTTCCACAAAG

Alignment

ORF - retro_itri_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSETKNSPEYASFF--AVMGASSAMIFSALGAAYGTAKSGTGIAAMSVMRPELIMKSIIP-VVMAGIIAI
          MSETKN.PE.ASFF......ASSAMIFSALGA.Y...KSGTGIAA..VM.PE.IMKSI.P.V.MAG..AI
Retrocopy MSETKNNPEKASFFFSEITSASSAMIFSALGATYCMPKSGTGIAAV*VMKPEKIMKSITP<VFMAGLFAI

Parental  YGLVVAVLIANSLNDGISLYRSFLQLGAGLSVGLSGLA-AGFAIGIVGDAGVRGTAQQPRLFVGMILILI
          YGLVVAVLIANSLNDG.SLYRS.LQLGAG.SVGLSGLA.AGFAIGIVGDAGV.GTAQQP.LFVGMILILI
Retrocopy YGLVVAVLIANSLNDGMSLYRSLLQLGAGQSVGLSGLA>AGFAIGIVGDAGVQGTAQQP*LFVGMILILI

Parental  FAEVLGLYGLIVALILSTK
          F.EVLGL.GLI.ALILSTK
Retrocopy FTEVLGL*GLIMALILSTK

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_387 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_387 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 15 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026428	1 retrocopy	retro_btau_1638,
Homo sapiens	ENSG00000185883	2 retrocopies	retro_hsap_1798, retro_hsap_3462,
Gorilla gorilla	ENSGGOG00000028600	2 retrocopies	retro_ggor_1323, retro_ggor_2335,
Macropus eugenii	ENSMEUG00000004597	2 retrocopies	retro_meug_1428, retro_meug_1837,
Myotis lucifugus	ENSMLUG00000026715	2 retrocopies	retro_mluc_2507, retro_mluc_294,
Monodelphis domestica	ENSMODG00000015439	5 retrocopies	retro_mdom_1669, retro_mdom_1739, retro_mdom_507, retro_mdom_84, retro_mdom_982,
Mus musculus	ENSMUSG00000024121	2 retrocopies	retro_mmus_2726, retro_mmus_2888,
Nomascus leucogenys	ENSNLEG00000009416	2 retrocopies	retro_nleu_1692, retro_nleu_2770,
Procavia capensis	ENSPCAG00000015060	1 retrocopy	retro_pcap_148,
Pan troglodytes	ENSPTRG00000007653	2 retrocopies	retro_ptro_1204, retro_ptro_2346,
Rattus norvegicus	ENSRNOG00000006542	1 retrocopy	retro_rnor_118,
Sarcophilus harrisii	ENSSHAG00000014251	1 retrocopy	retro_shar_194,
Ictidomys tridecemlineatus	ENSSTOG00000013420	3 retrocopies	retro_itri_119, retro_itri_387 , retro_itri_691,
Drosophila melanogaster	FBgn0262736	3 retrocopies	retro_dmel_3, retro_dmel_38, retro_dmel_65,
Caenorhabditis elegans	R10E11.2	2 retrocopies	retro_cele_1, retro_cele_5,