RetrogeneDB ID: retro_itri_1566

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393543.1:244512..244905(+)
• Located in intron of: ENSSTOG00000009528

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD8
• Ensembl ID: ENSSTOG00000001221
• Aliases: None
• Description: COMM domain containing 8 [Source:HGNC Symbol;Acc:26036]

Sequence

>retro_itri_1566
ACCACAGAATGGATGAATGTTTTAGAAAATGTTACCAAAATTTTTAAAGCTCTAGTTGGTAAAAATTTATTCGATGAAGA
GACACTTCAGCAATTGAATCATTTGAATTCATCTCATCAAGAAGCTATCATGAAATGCTTGAAAAGTAGGAAAGATGAAA
TCAAGCAAGTTCTTTTAAAGGAAATAGTTGATATTTCTTCTGCACAGTTACAGGATTTTGATTGGCAGTTAAAGCTTGCA
CTTTCTAGTGACAAGATTGCTACTTTACAAATGCCACTCTTAAACCTTCATCTAGATGTAAAAGAAAATGGTGAAGTAAA
ACCATATTTGGTTGAAATGAGTAAAGAAGAGCTGCAGAATCTAATAAATTCCTTGGAAGCAGCTAATAAGGTG

Alignment

ORF - retro_itri_1566 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.66 %
• Parental protein coverage: 73.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STEWMNVLEDVTKFFKALVGKNLSDEETLQQLNHLNSSHQEAIMKCLKSRKNEIKQVLLREIVDISSAQL
          .TEWMNVLE.VTK.FKALVGKNL.DEETLQQLNHLNSSHQEAIMKCLKSRK.EIKQVLL.EIVDISSAQL
Retrocopy TTEWMNVLENVTKIFKALVGKNLFDEETLQQLNHLNSSHQEAIMKCLKSRKDEIKQVLLKEIVDISSAQL

Parental  QDFDWQLKLALSSDKIATLQMPLLNLHLDVKENGEVKPYSVEMSKEELQNLINSLEAANKV
          QDFDWQLKLALSSDKIATLQMPLLNLHLDVKENGEVKPY.VEMSKEELQNLINSLEAANKV
Retrocopy QDFDWQLKLALSSDKIATLQMPLLNLHLDVKENGEVKPYLVEMSKEELQNLINSLEAANKV

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_1566 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1566 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001348	1 retrocopy	retro_btau_579,
Echinops telfairi	ENSETEG00000020257	3 retrocopies	retro_etel_1416, retro_etel_182, retro_etel_210,
Felis catus	ENSFCAG00000023811	1 retrocopy	retro_fcat_421,
Myotis lucifugus	ENSMLUG00000011376	1 retrocopy	retro_mluc_1158,
Macaca mulatta	ENSMMUG00000021777	1 retrocopy	retro_mmul_434,
Ochotona princeps	ENSOPRG00000000739	1 retrocopy	retro_opri_805,
Ictidomys tridecemlineatus	ENSSTOG00000001221	1 retrocopy	retro_itri_1566 ,