RetrogeneDB ID: retro_itri_103

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393554.1:1613789..1614458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027334
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CXorf56
• Ensembl ID: ENSSTOG00000011579
• Aliases: None
• Description: chromosome X open reading frame 56 [Source:HGNC Symbol;Acc:26239]

Sequence

>retro_itri_103
ATGCCTAAAGTAGTGTCTCGGTCGGTTGTCTGCTCCGATACCCGGGACCGCGAGGAATATGACGATGGTGAGAAGCCCCT
CCACGTCTACTACTGTTTGTGTGGCCAGATGGTCCTGGTGCTGGATTGTCAGTTAGAGAAGTTGCCCATGAGGCCTCGAG
ACCGATCCCGTGTGATTGATGCTGCTAAACATGCTCACAAATTTTGTAATACAGAAGATGAGGAGACTGTGTATCTTCGA
AGGCCTGAAGGCATTGAACGACAATACAGGAAGAAGTGTGCCAAGTGTGGACTACCTCTCTTCTACCAGTCCCAGCCGAA
GAATGCCCCTGTGACCTTCATCGTGGATGGAGCAGTAGTGAAATTTGGTCAGGGTTTTGGGAAAACAAATATATATACTC
AGAAACAAGAGCCTCCAAAGAAGGTGATGATGACCAAACGGACCAAAGACATGGGCAAGTTCAGCTCTGTCACCGTGTCT
ACCATTGATGAAGAGGAAGAGGAGATTGAGGCTAGGGAAGTTGCTGACTCCTATGCACAGAATGCCAAAGTGATTGAAAA
ACAGCTGGAGCGCAAAGGCATGAGCAAGAGACGACTGCAAGAGCTGGCTGAACTGGAAGCCAAGAAAGCTAAAATGAAGG
GGACCTTGATTGACAACCAGTTCAAATGA

Alignment

ORF - retro_itri_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
          MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
Retrocopy MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN

Parental  TEDEETMYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
          TEDEET.YLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
Retrocopy TEDEETVYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK

Parental  KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEAKKA
          KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEAKKA
Retrocopy KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEAKKA

Parental  KMKGTLIDNQFK
          KMKGTLIDNQFK
Retrocopy KMKGTLIDNQFK

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_103 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_103 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 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005111	1 retrocopy	retro_cjac_311,
Homo sapiens	ENSG00000018610	1 retrocopy	retro_hsap_4044,
Gorilla gorilla	ENSGGOG00000013324	1 retrocopy	retro_ggor_2711,
Latimeria chalumnae	ENSLACG00000012468	1 retrocopy	retro_lcha_59,
Myotis lucifugus	ENSMLUG00000015751	1 retrocopy	retro_mluc_72,
Macaca mulatta	ENSMMUG00000022665	1 retrocopy	retro_mmul_2333,
Mus musculus	ENSMUSG00000006423	1 retrocopy	retro_mmus_1715,
Nomascus leucogenys	ENSNLEG00000014862	1 retrocopy	retro_nleu_2057,
Otolemur garnettii	ENSOGAG00000012474	1 retrocopy	retro_ogar_145,
Pongo abelii	ENSPPYG00000020670	1 retrocopy	retro_pabe_177,
Pan troglodytes	ENSPTRG00000022224	1 retrocopy	retro_ptro_104,
Sorex araneus	ENSSARG00000003163	1 retrocopy	retro_sara_5,
Sarcophilus harrisii	ENSSHAG00000006319	1 retrocopy	retro_shar_16,
Ictidomys tridecemlineatus	ENSSTOG00000011579	1 retrocopy	retro_itri_103 ,
Tarsius syrichta	ENSTSYG00000008043	1 retrocopy	retro_tsyr_634,
Tursiops truncatus	ENSTTRG00000013101	2 retrocopies	retro_ttru_231, retro_ttru_77,