RetrogeneDB ID: retro_itri_675

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:6561215..6561757(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME6
• Ensembl ID: ENSSTOG00000002690
• Aliases: None
• Description: NME/NM23 nucleoside diphosphate kinase 6 [Source:HGNC Symbol;Acc:20567]

Sequence

>retro_itri_675
ATGACCTCAATTTTGTGAAGCCCTAAGGCTCTGCAGCTTACTCTAGCCCTGATCAAGCCTGATGTAGTTGCTCACCCATT
GATTCTGGAGGCTGTTCATCAGCAGATTCTGAGCAGCAAGTTCCTTATTGTACGAATGAGAGAACTACTATGGAGAAAGG
AAGATTGCCAGAAGTTTTACAAGGAACATGAAGAGCATTTTTTCTATCAGCGACTGGTGGAGTTCATGGCCGGTGGACCA
ATCCGAGCTTATATCCTTGCTCACGAGGATGCCATCCAGCTTTGGAGGACACTGATGGGGCCCACCAGAGTGTTTCGAGC
ATGCCACATGTCCCCAGATTCAATTCGTAGGAGTTTTGGCACCTCAGACACGCGCAACACCACCCATGGCTCAGACTCTG
TGGTTTTAGCCAGCAGAGAGATTGCAGCCTTCTTTCCTGACTTCAGTGAAAGTGCTGGTATGAGGAGGAAGAGCCCCAGT
TGTGCTGTGGTCCTGTGTGCTACACAGAGGGAGGCATCCACTGTGTAGCTTGAACAGGAGGC

Alignment

ORF - retro_itri_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSILRSPKALQLTLALIKPDAVAHPLILEAVHQQILSNKFLIVRMRELLWRKEDCQKFYKEHEGRFFYQ
          MTSIL.SPKALQLTLALIKPD.VAHPLILEAVHQQILS.KFLIVRMRELLWRKEDCQKFYKEHE..FFYQ
Retrocopy MTSIL*SPKALQLTLALIKPDVVAHPLILEAVHQQILSSKFLIVRMRELLWRKEDCQKFYKEHEEHFFYQ

Parental  RLVEFMASGPIRAYILAHKDAIQLWRTLMGPTRVFRARHMAPDSIRGSFGLTDTRNTTHGSDSVVSASRE
          RLVEFMA.GPIRAYILAH.DAIQLWRTLMGPTRVFRA.HM.PDSIR.SFG..DTRNTTHGSDSVV.ASRE
Retrocopy RLVEFMAGGPIRAYILAHEDAIQLWRTLMGPTRVFRACHMSPDSIRRSFGTSDTRNTTHGSDSVVLASRE

Parental  IAAFFPDFSEQR-WYEEEEPQLRCGPVCYTEGGIHCAVGTGG
          IAAFFPDFSE...WYEEEEPQL.CGPVCYTEGGIHC...TGG
Retrocopy IAAFFPDFSESA<WYEEEEPQLCCGPVCYTEGGIHCVA*TGG

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_675 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_675 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000032478	1 retrocopy	retro_mmus_2376,
Sus scrofa	ENSSSCG00000011347	1 retrocopy	retro_sscr_1076,
Ictidomys tridecemlineatus	ENSSTOG00000002690	1 retrocopy	retro_itri_675 ,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629,