RetrogeneDB ID: retro_itri_994

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393357.1:1402860..1403198(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPA
• Ensembl ID: ENSSTOG00000025168
• Aliases: None
• Description: centromere protein A [Source:HGNC Symbol;Acc:1851]

Sequence

>retro_itri_994
CCAGAGCGGGGCACCTCCCTAGGTTCTTTATTCTGTCAATACAGTCACTGAAGATGTGATTGGATTAAGGAAATCATAAA
GCTACAGAAGAGCACAGACCTCTTGATAAGAAAGTACCCCTTCAATCACCTGGTTAAATAAATACATATTAAATTCACCG
TGGTGTGGACTTCAGTTGGCAAGCCCAGGCCCTGTTGGCCCTTCAAGAGGTAGCAGAAGCGTTTTTAGTTTTCCTGTTTG
AGGATGCCTACCTCCTCTCCTTACATGCTAGAGTCACTCTCATCCCCAAGGATGTGCAGCCAGCCTGGAGGACCTGTGGC
ATTGAGGAAGGACTTGGC

Alignment

ORF - retro_itri_994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 82.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRREASLGSSSRQHSRRRIRWIKEIKNLQKSTDLLIRRYPFSRLAREICMKFT-RGVDFSWQAQALLALQ
          P.R..SLGS...Q.S..R..WIKEI..LQKSTDLLIR.YPF..L...I..KFT.RGVDFSWQAQALLALQ
Retrocopy PERGTSLGSLFCQYSH*RCDWIKEIIKLQKSTDLLIRKYPFNHLVK*IHIKFT<RGVDFSWQAQALLALQ

Parental  EAAEAFLVHLFEDAYLLSLHAGRVTLFPKDVQLARRIRGIEEGLG
          E.AEAFLV.LFEDAYLLSLHA.RVTL.PKDVQ.A.R..GIEEGLG
Retrocopy EVAEAFLVFLFEDAYLLSLHA-RVTLIPKDVQPAWRTCGIEEGLG

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_994 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_994 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023938	1 retrocopy	retro_btau_947,
Choloepus hoffmanni	ENSCHOG00000004496	3 retrocopies	retro_chof_2096, retro_chof_2448, retro_chof_4,
Ornithorhynchus anatinus	ENSOANG00000000516	1 retrocopy	retro_oana_72,
Otolemur garnettii	ENSOGAG00000024154	2 retrocopies	retro_ogar_3405, retro_ogar_3505,
Ictidomys tridecemlineatus	ENSSTOG00000025168	2 retrocopies	retro_itri_835, retro_itri_994 ,
Tarsius syrichta	ENSTSYG00000010334	1 retrocopy	retro_tsyr_2007,
Tursiops truncatus	ENSTTRG00000010278	2 retrocopies	retro_ttru_590, retro_ttru_784,