RetrogeneDB ID: retro_itri_835

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393331.1:1824648..1824866(+)
• 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_835
CTGCCGAAGAGCACGGATCTCTTGGCAAGCAGGTACCCCCTGGGCCACCTGGCAAGAAGAATACCTATTCAATTCACTCA
TGGTGTAGACATCAGTGGGCAAGCCCAGGCCCACTGAGGCCCCTTAAGTGGCTCCAGAGCATTTCCAGTTTGCTCTTTTA
GGGTGCCTAACTCCTTTCCTTACAGGGCTGAGCCACCCTCTTCCCCAAGGATGTGCAG

Alignment

ORF - retro_itri_835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.33 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQKSTDLLIRRYPFSRLAREICMKFTRGVDFSWQAQALLALQEAAEAFLV-HLFEDAYLLSLHAGRVTLF
          L.KSTDLL..RYP...LAR.I...FT.GVD.S.QAQA.........AF.V..LF..A.LLSL..G..TLF
Retrocopy LPKSTDLLASRYPLGHLARRIPIQFTHGVDISGQAQAH*GPLSGSRAFPV<LLF*GA*LLSLQ-G*ATLF

Parental  PKDVQ
          PKDVQ
Retrocopy PKDVQ

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_835 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_835 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,