RetrogeneDB ID: retro_itri_1127

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393382.1:4067768..4068194(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000008829
• Aliases: None
• Description: None

Sequence

>retro_itri_1127
CATTGCCAGGGCATGATGGTGGTGGGTACTGGCAGCTCGCTGGCTCTGTTCTCTCTCCTGTCCCTGCTGCTCTTCACAGG
GATGCAGATGTACAGCCACCAGCTGGCCTCCACCAAGTGGCTCATCATGGAGGGGGGCATGCTGGGCTCTGGCCTTTTCT
TCTCTCTCACAGCCTTCAATAATCTGGAGAATATGGTCTTTGGCAAAGGATTCCAAGCAAAGATCTTCCCTGAGATTCTC
CTCTGCCTCCTGTTGGCTCTCTTTGCATCTGGCCTCATCCACTGAGTCTGTGTCACCACCTGCTTCCTCTTCTCCATGGT
TGGTCTGTACTACATCAACATCAACAAGATCTCCTCTACTCTGCACCAGGCAAGAGCTCCAGTCCTCACATCAGCCAAAG
TCACTGGCAAGGGCAAGAAGAGAAAT

Alignment

ORF - retro_itri_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.71 %
• Parental protein coverage: 64.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HCRGMMVVGTGTSLALSSLLSLLLFAGMQMYSRQLASTEWLTIQGGLLGSGLFVFSLTAFNNLENLVFGK
          HC.GMMVVGTG.SLAL.SLLSLLLF.GMQMYS.QLAST.WL...GG.LGSGLF.FSLTAFNNLEN.VFGK
Retrocopy HCQGMMVVGTGSSLALFSLLSLLLFTGMQMYSHQLASTKWLIMEGGMLGSGLF-FSLTAFNNLENMVFGK

Parental  GFQAKIFPEILLCLLLALFASGLIHRVCVTTCFIFSMVGLYY--INKISSTLYQATAPVLTPAKVTGKGK
          GFQAKIFPEILLCLLLALFASGLIH.VCVTTCF.FSMVGLYY..INKISSTL.QA.APVLT.AKVTGKGK
Retrocopy GFQAKIFPEILLCLLLALFASGLIH*VCVTTCFLFSMVGLYYININKISSTLHQARAPVLTSAKVTGKGK

Parental  KRN
          KRN
Retrocopy KRN

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_1127 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1127 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011336	1 retrocopy	retro_amel_1789,
Canis familiaris	ENSCAFG00000017055	1 retrocopy	retro_cfam_1487,
Callithrix jacchus	ENSCJAG00000009017	1 retrocopy	retro_cjac_1289,
Felis catus	ENSFCAG00000025085	3 retrocopies	retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens	ENSG00000163463	1 retrocopy	retro_hsap_2100,
Gorilla gorilla	ENSGGOG00000009303	1 retrocopy	retro_ggor_1635,
Macaca mulatta	ENSMMUG00000012180	2 retrocopies	retro_mmul_745, retro_mmul_987,
Mustela putorius furo	ENSMPUG00000005647	1 retrocopy	retro_mputfur_1653,
Nomascus leucogenys	ENSNLEG00000011864	1 retrocopy	retro_nleu_1306,
Oryctolagus cuniculus	ENSOCUG00000000347	1 retrocopy	retro_ocun_157,
Otolemur garnettii	ENSOGAG00000030271	1 retrocopy	retro_ogar_1306,
Pongo abelii	ENSPPYG00000000756	1 retrocopy	retro_pabe_1999,
Pan troglodytes	ENSPTRG00000001410	1 retrocopy	retro_ptro_1541,
Rattus norvegicus	ENSRNOG00000020542	1 retrocopy	retro_rnor_2128,
Ictidomys tridecemlineatus	ENSSTOG00000008829	1 retrocopy	retro_itri_1127 ,
Tarsius syrichta	ENSTSYG00000013228	2 retrocopies	retro_tsyr_1096, retro_tsyr_531,