RetrogeneDB ID: retro_itri_1376

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393464.1:3794595..3795538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM17
• Ensembl ID: ENSSTOG00000013591
• Aliases: None
• Description: RNA binding motif protein 17 [Source:HGNC Symbol;Acc:16944]

Sequence

>retro_itri_1376
GCAGGGGAAGTTCTAATCCACTTAGCTGATGAATATGATCCTATGTTTCCTAATGATCATGAGAAAGTAGTGAAACTCCA
AAAAGAGGAATGACAAAGCTGGAAAGACAGAAGGAAATAGAGGAAAGGGGGAAGGAGGCATAAAGACAAACACGGAGCAA
GTGGGTTTTCAGGGCGACCAGATCCAGATTCTGATGAGGATGAAGATTACGAGCGAGAGAGGAGGGAAAAGAAGTATGGG
AGGAGCTGCCATCGCCCCCACCTACTTCTCTTGTAGAGAAAGACAAAAAGTTACCCCGAGATTTTCCTTATGAAGAGGAC
TCAAGACCTTGATCACCATCTTCCAAAGCTGTATTCCTCCTGCAGTATATGAGGAACAGGATAGACCGAGATCTCCAATT
GAGCCTAGCAACTCTTTCCTTCTAACACGGATGGCACAGTAGCATCCAAGATCATGCAAAAGTGTGGCTTCCGGGAAGGC
CAGGGTCTGGGGAAGCAGGAGCAGGGTCCGAGTACTGCATTGTCAGTGGAGAAGACCTGCAAGGAGGGCGTCAAGATCAT
TGTGGGTGATGCCACGGAGAAGCGCCAGTCTCAGGATCCATCCAAGAAGTCAGATTCAAATCCATTAACTTACATACTTA
AGTGTCTTACCAAGTGATCCTACTGAGGAACATGGTTGGTGCAGGAGAGGTAGATGAAGACTTGGAAATTGAAACCAAAG
AGAATGTGAAAAAAAAAATGGCAAAGTTGGAAAATGTATGGTATTTGAAATTCCTGGTGCTCCTGATAATGAGGCAGTAT
GAATATTTTTAGAATTTGAGAGAGTTGAATCAGCAATTAAAGCTGTTGTTGATTTGAATGGGAGGTATTTTAGTGGAAGA
GTGGTATAAGCATGTTTCTACAATTTGGATAAATTTAGGGTCTATGATTTGGCTGAACAAGTT

Alignment

ORF - retro_itri_1376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 78.27 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEEREKRRKDRHEASGFSRRPDPDSDED
          AGEVLI.LADEYDPMFPND.EKVVK.Q.EE.Q................R.KD.H.ASGFS.RPDPDSDED
Retrocopy AGEVLIHLADEYDPMFPNDHEKVVKLQKEE*QSWKD---RRK*RKGGRRHKDKHGASGFSGRPDPDSDED

Parental  EDYERERR-KRSMGGAAIA-PPTSLVEKDKELPRDFPYEEDSRPRSQSSKA-AIPPPVYEEQDRPRSPTG
          EDYERERR.KRSMGGAAIA.PPTSLVEKDK.LPRDFPYEEDSRP.S.SSKA..IPP.VYEEQDRPRSP..
Retrocopy EDYERERR>KRSMGGAAIA>PPTSLVEKDKKLPRDFPYEEDSRP*SPSSKA<CIPPAVYEEQDRPRSPIE

Parental  PSNSFL-ANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKIIVGDATEKGESQDASKK
          PSNSFL..N..GTVA.KIMQK.GFREGQGLGK.EQG.STALSVEKT.K.G.KIIVGDATEK..SQD.SKK
Retrocopy PSNSFL<SNTDGTVASKIMQKCGFREGQGLGKQEQGPSTALSVEKTCKEGVKIIVGDATEKRQSQDPSKK

Parental  SDSNPLTEILKCPTK-VVLLRNMVGAGEVDEDLEVETKE-EC-EKYGKVGKCVIFEIPGAPDDEAVRIFL
          SDSNPLT.ILKC.TK.V.LLRNMVGAGEVDEDLE.ETKE.EC....GKVGKC..FEIPGAPD.EAV.IFL
Retrocopy SDSNPLTYILKCLTK<VILLRNMVGAGEVDEDLEIETKE<ECXXXXGKVGKCMVFEIPGAPDNEAV*IFL

Parental  EFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLAEQV
          EFERVESAIKAVVDLNGRYF.GRVV.ACFYNLDKFRV.DLAEQV
Retrocopy EFERVESAIKAVVDLNGRYFSGRVV*ACFYNLDKFRVYDLAEQV

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_1376 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1376 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 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376 ,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,