RetrogeneDB ID: retro_itri_843

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393332.1:8766095..8766580(+)
• Located in intron of: ENSSTOG00000006129

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR61
• Ensembl ID: ENSSTOG00000007784
• Aliases: None
• Description: WD repeat domain 61 [Source:HGNC Symbol;Acc:30300]

Sequence

>retro_itri_843
TTTTCTTTGGACATGAGAGAAAAATTCATTCTTAGTATTGTGTATATTCCTGATGGGAAATATCTGACCAGTAGAGTTAT
AAATGGAATTATCAATATTTTTGATATTGCAACTGGAAAACTTCTGCATACACTGGAAGGTCACACTTCATGCATCTGCT
CCTTGACCTTTTCCTGAACTCTCAATTCTTTATCACTGCTTCAGATGTTCAATACATCAAGATCTACTACCAAGCTAATT
TGGCTGGCATGCTGCATGGCCATGCCTCCCAGGTATTGAACATCCAGTTTTGTCCTGAAGACACTAATTTTGCTTCTGGT
TCATCTGACAAAAATATGAAAATTTGGGATGTTGGAAAGAGAATGGATACTCACACTCTCTTAGATTACCAGAATCAGTT
CTGAAGACTAAAATACAACGGAAATGGTTCTAAAAGTTTGTGTGTTGGAGATGACCAGGAAATTCACATCTATGATTGTC
CAATT

Alignment

ORF - retro_itri_843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.48 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YSLDTRGKFILSIAYSPDGKYLASGAIDGIINIFDIATGKLLHTLEGHAMPIRSLTFS-PDSQLLVTASD
          .SLD.R.KFILSI.Y.PDGKYL.S..I.GIINIFDIATGKLLHTLEGH...I.SLTFS...SQ...TASD
Retrocopy FSLDMREKFILSIVYIPDGKYLTSRVINGIINIFDIATGKLLHTLEGHTSCICSLTFS<LNSQFFITASD

Parental  DGYIKIYDVQHANLAGTLSGHASWVLNVAFCPDDTHFVSSSSDKSVKVWDVGTRTCVHTFFDHQDQVWGV
          ..YIKIY....ANLAG.L.GHAS.VLN..FCP.DT.F.S.SSDK..K.WDVG.R...HT..D.Q.Q....
Retrocopy VQYIKIY--YQANLAGMLHGHASQVLNIQFCPEDTNFASGSSDKNMKIWDVGKRMDTHTLLDYQNQF*RL

Parental  KYNGNGSKIVSVGDDQEIHIYDCPI
          KYNGNGSK...VGDDQEIHIYDCPI
Retrocopy KYNGNGSKSLCVGDDQEIHIYDCPI

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_843 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_843 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014230	3 retrocopies	retro_cfam_1378, retro_cfam_1422, retro_cfam_910,
Macropus eugenii	ENSMEUG00000015991	1 retrocopy	retro_meug_744,
Oryctolagus cuniculus	ENSOCUG00000009040	1 retrocopy	retro_ocun_1570,
Ictidomys tridecemlineatus	ENSSTOG00000007784	1 retrocopy	retro_itri_843 ,
Tupaia belangeri	ENSTBEG00000009390	1 retrocopy	retro_tbel_48,