RetrogeneDB ID: retro_itri_11

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393332.1:7120015..7120972(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021873
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000007638
• Aliases: None
• Description: None

Sequence

>retro_itri_11
ATGCCGAATATCAAAATCTTCAGCGGCAGCTCTCATCAGGACCTATCCCAGAAAATTGCTGACCGCCTGGGCCTGGAGCT
AGGCAAGGTGGTGACTAAGAAATTCAGCAACCAGGAGACCTGTGTGGAAATTGGTGAAAGTGTACATGGAGAAGATGTCT
ACATCGTTCAAAGTGGTTGTGGTGAAATCAACGACAATCTAATGGAGCTTTTGATCATGATTAATGCCTGCAAGATTGCT
TCAGCCAGCCGGGTTACTGCAGTCATCCCATGTTTCCCTTATGCCCGGCAGGATAAGAAGGATAAGAGCCGAGCACCAAT
CTCAGCTAAGCTTGTTGCAAATATGCTGTCTGTAGCTGGTGCAGATCATATTATCACCATGGATCTACATGCTTCTCAAA
TTCAGGGCTTTTTTGATATCCCAGTGGACAATTTGTATGCAGAGCCAGCTGTCCTGAAGTGGATTAGGGAGAATATATCT
GAGTGGAGGAACTGCACTATTGTGTCACCTGATGCTGGTGGAGCCAAGAGAGTGACCTCCATTGCAGACCGGTTGAATGT
GGACTTTGCCTTGATTCACAAAGAACGGAAGAAGGCTAATGAAGTGGACCGCATGGTGCTAGTGGGAGATGTGAAGGATC
GAGTCGCTATCCTTGTGGATGACATGGCTGACACATGTGGCACAATTTGTCATGCCGCTGACAAACTTCTCTCAGCTGGA
GCGACCAGAGTTTATGCTATCTTGACTCATGGAATCTTTTCTGGCCCAGCCATTTCTCGAATCAATAATGCATGTTTTGA
AGCAGTAGTGGTCACCAATACCATACCTCAGGAGGACAAGATGAAGCATTGCTCTAAAATACAGGTGATTGACATCTCTA
TGATCCTTGCGGAAGCCATCAGGAGAACTCATAATGGGGAATCTGTTTCCTACCTATTCAGTCATGTTCCTTTATAA

Alignment

ORF - retro_itri_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL
          MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESV.GEDVYIVQSGCGEINDNLMEL
Retrocopy MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVHGEDVYIVQSGCGEINDNLMEL

Parental  LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
          LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
Retrocopy LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI

Parental  PVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD
          PVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD
Retrocopy PVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD

Parental  VKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK
          VKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK
Retrocopy VKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK

Parental  MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
Retrocopy MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL

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_11 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_11 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 25 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002784	1 retrocopy	retro_amel_22,
Bos taurus	ENSBTAG00000019703	3 retrocopies	retro_btau_157, retro_btau_1686, retro_btau_914,
Canis familiaris	ENSCAFG00000017976	1 retrocopy	retro_cfam_1443,
Equus caballus	ENSECAG00000024711	2 retrocopies	retro_ecab_433, retro_ecab_73,
Felis catus	ENSFCAG00000012286	1 retrocopy	retro_fcat_394,
Homo sapiens	ENSG00000147224	1 retrocopy	retro_hsap_10,
Gorilla gorilla	ENSGGOG00000012418	1 retrocopy	retro_ggor_2583,
Macropus eugenii	ENSMEUG00000010071	2 retrocopies	retro_meug_1612, retro_meug_443,
Microcebus murinus	ENSMICG00000001929	5 retrocopies	retro_mmur_1223, retro_mmur_1422, retro_mmur_514, retro_mmur_810, retro_mmur_90,
Myotis lucifugus	ENSMLUG00000015498	2 retrocopies	retro_mluc_107, retro_mluc_356,
Macaca mulatta	ENSMMUG00000004674	3 retrocopies	retro_mmul_1204, retro_mmul_1619, retro_mmul_305,
Mustela putorius furo	ENSMPUG00000003793	2 retrocopies	retro_mputfur_183, retro_mputfur_430,
Mus musculus	ENSMUSG00000031432	2 retrocopies	retro_mmus_19, retro_mmus_33,
Nomascus leucogenys	ENSNLEG00000013911	2 retrocopies	retro_nleu_1456, retro_nleu_217,
Oryctolagus cuniculus	ENSOCUG00000012391	3 retrocopies	retro_ocun_430, retro_ocun_867, retro_ocun_912,
Ochotona princeps	ENSOPRG00000013140	1 retrocopy	retro_opri_704,
Pongo abelii	ENSPPYG00000020612	2 retrocopies	retro_pabe_3061, retro_pabe_46,
Pan troglodytes	ENSPTRG00000022163	2 retrocopies	retro_ptro_2600, retro_ptro_2612,
Rattus norvegicus	ENSRNOG00000025166	2 retrocopies	retro_rnor_249, retro_rnor_341,
Sus scrofa	ENSSSCG00000012560	1 retrocopy	retro_sscr_1068,
Ictidomys tridecemlineatus	ENSSTOG00000006056	1 retrocopy	retro_itri_1668,
Ictidomys tridecemlineatus	ENSSTOG00000007638	2 retrocopies	retro_itri_11 , retro_itri_173,
Tarsius syrichta	ENSTSYG00000013556	2 retrocopies	retro_tsyr_1063, retro_tsyr_1567,
Tursiops truncatus	ENSTTRG00000003835	2 retrocopies	retro_ttru_307, retro_ttru_485,
Vicugna pacos	ENSVPAG00000000255	1 retrocopy	retro_vpac_274,