RetrogeneDB ID: retro_itri_19

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393673.1:113729..114479(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023488
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000006891
• Aliases: None
• Description: None

Sequence

>retro_itri_19
ATGGCTCAGAGAAAGGAACTCGACCTAACTGGCGTCAAGCAAAACACCCGAATGTGGCTAGTCAAGGTTCCTAAATATCT
GTCACAGCAATGGGCTAAAGCCCCTGGAAGAGGTGAAGTTGGAAAACTGAGGATTGCCAAGAATCAAGGAAAGACTGAAG
TATCATTTACTTTGAATGAGGATCTTGCAAATTTTCATGATATTGGTGGAAAACCAGCCTCAGTCAGTGCTCCTAGAGAA
CATCGGTTTGTCTTGCAAAGGGTTGAAGGACAGATGTTAACAGTATTTTCTGAGAGCTCCTCAGGTAAACTCTCATTAGA
AGGAAAGGCGGAACAAAGAGTCGAATGCCGACCTGTTGCCAGTGAAAACTACATGAGATTAAAGAGATTGCAAATAGAAG
AATCTTCCAAACCTGGAAGGGTATCACAACAACTGGAGAAAGCTGTAACAACAAATTACAAGCCTGTTGCTGATCACCAA
TGTAATATTGAGTATCAAAAGAAAAAGAAAAATGATGGAAAGCGAGTTAAGGCTGATAAACAACATGTATTAGACACGCT
GTTTTGTGCCTTTGAGAAACATCAGTATTATAATCTTAAGGACTTGGTGGACATCACAAAACAACCCGTGGGATATCTAA
AGGACATCTTGAAGGAAATTGGAATTTACAGTACGAAAGGGATTCACAAAAACACATGGGAGCTGAAGCCAGAATATAGG
CATTATCAAGGAGAAGAAAAGAGCAATTGA

Alignment

ORF - retro_itri_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLKRLQIEESSKPVRLSQQLEKVVTTNYKPVANHQYNIEYERKKKEDGKRARADKQHVLDMLFSAFEKH
          MRLKRLQIEESSKP.R.SQQLEK.VTTNYKPVA.HQ.NIEY..KKK.DGKR..ADKQHVLD.LF.AFEKH
Retrocopy MRLKRLQIEESSKPGRVSQQLEKAVTTNYKPVADHQCNIEYQKKKKNDGKRVKADKQHVLDTLFCAFEKH

Parental  QYYNLKDLVDITKQPVGYLKDILKEIGIQNVKGIHKNTWELKPEYRHYQGEEKSD
          QYYNLKDLVDITKQPVGYLKDILKEIGI...KGIHKNTWELKPEYRHYQGEEKS.
Retrocopy QYYNLKDLVDITKQPVGYLKDILKEIGIYSTKGIHKNTWELKPEYRHYQGEEKSN

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_19 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_19 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 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Bos taurus	ENSBTAG00000034495	2 retrocopies	retro_btau_1753, retro_btau_208,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Callithrix jacchus	ENSCJAG00000019220	2 retrocopies	retro_cjac_1351, retro_cjac_2990,
Felis catus	ENSFCAG00000002105	1 retrocopy	retro_fcat_526,
Homo sapiens	ENSG00000188342	2 retrocopies	retro_hsap_2990, retro_hsap_368,
Gorilla gorilla	ENSGGOG00000006657	2 retrocopies	retro_ggor_2070, retro_ggor_379,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Macaca mulatta	ENSMMUG00000012634	2 retrocopies	retro_mmul_1913, retro_mmul_483,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Otolemur garnettii	ENSOGAG00000012517	1 retrocopy	retro_ogar_2772,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pan troglodytes	ENSPTRG00000005840	3 retrocopies	retro_ptro_2022, retro_ptro_288, retro_ptro_2932,
Pteropus vampyrus	ENSPVAG00000014092	1 retrocopy	retro_pvam_1490,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19 ,
Tursiops truncatus	ENSTTRG00000002729	2 retrocopies	retro_ttru_1003, retro_ttru_850,