RetrogeneDB ID: retro_itri_1085

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393372.1:4615141..4615732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMA16
• Ensembl ID: ENSSTOG00000024763
• Aliases: None
• Description: translation machinery associated 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25638]

Sequence

>retro_itri_1085
ATGCCTGAAGTACCAAAGGGAGGAAATACAGGACAGGAAAGAAGTCATCCATCCAAGTAGTAGAAAATCAGCTCTGAGAA
AGGCCCACAAACAAGGAGAAAAAAATTAAAGAATGAAAAGGCCTTGCGTCTCCATCTTATTGGTGGGAAAAACTGCAGTG
GTTTCAAAATCATCTGGATTCCCCCCAAATTGGGGCATTCAAACAAAGATGCTTGTGAATTAGTGGAAAGGTACTTACAT
AGATTTAGCAGTGAGCTGGAGCAGATGGAATTACACGCCAGCATCAGGGACAGGTGGGGAAGGCGGCACTTTTCCGTTAT
CAAGTAGCCAATGGAGCACAGTGACCGCAGTCTGAAGGATGTGGCCTTGAGATGCCAGGCATCTTAAATGCAAAGGATCT
GAAGAGTTTTAGGGAATGGGATTTTGATCGGAAGAAACTGCCAAAAATGAAAACGCGAAAACTCTGTGCTAATGATGCAG
TTCCTAAGAAAGGCAAGAGGGAAAGTATTTTAACTGTAGACAAAAAATTTAGGGGACTCGGAACTAAAAGGTGAATCAAA
TGACTCAGCCAAAGAAATGACCCCAATAGCC

Alignment

ORF - retro_itri_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKVPKGRSTGQEKKVIHPYSRKAAQITRETHKQDKKEKLKNEKALRLNLIGEK-LQWFQNHLDPKKLGY
          MP.VPKG..TGQE....HP...K...I..E...Q....KLKNEKALRL.LIG.K....F.....P.KLG.
Retrocopy MPEVPKGGNTGQERS--HP--SK**KISSEKGPQTRRKKLKNEKALRLHLIGGKNCSGFKIIWIPPKLGH

Parental  SKKDACELVERYLNRFSSELEQIELHNSIKDRQGRRHFSRETVIKQTMERERQ-QYEGYGLEIPDILNAN
          S.KDACELVERYL.RFSSELEQ.ELH.SI.DR.GRRHFS...VIK..ME.....Q.EG.GLE.P.ILNA.
Retrocopy SNKDACELVERYLHRFSSELEQMELHASIRDRWGRRHFS---VIK*PMEHSDR<QSEGCGLEMPGILNAK

Parental  NLKTFREWDFDLKKLPNIKMRKLCVNDAVPKKRKKKTILTID-KNLEELELKGESNDSDEEMTPVA
          .LK.FREWDFD.KKLP..K.RKLC.NDAVPKK.K...ILT.D.KNL...ELKGESNDS..EMTP.A
Retrocopy DLKSFREWDFDRKKLPKMKTRKLCANDAVPKKGKRESILTVD>KNLGDSELKGESNDSAKEMTPIA

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_1085 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1085 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 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006702	2 retrocopies	retro_chof_1717, retro_chof_2104,
Cavia porcellus	ENSCPOG00000001119	1 retrocopy	retro_cpor_444,
Dasypus novemcinctus	ENSDNOG00000006820	1 retrocopy	retro_dnov_489,
Echinops telfairi	ENSETEG00000009734	1 retrocopy	retro_etel_1378,
Homo sapiens	ENSG00000198498	2 retrocopies	retro_hsap_378, retro_hsap_879,
Gorilla gorilla	ENSGGOG00000025324	1 retrocopy	retro_ggor_713,
Macropus eugenii	ENSMEUG00000001134	3 retrocopies	retro_meug_1830, retro_meug_1895, retro_meug_396,
Macaca mulatta	ENSMMUG00000004482	2 retrocopies	retro_mmul_184, retro_mmul_276,
Monodelphis domestica	ENSMODG00000002170	1 retrocopy	retro_mdom_881,
Mus musculus	ENSMUSG00000025591	2 retrocopies	retro_mmus_299, retro_mmus_329,
Nomascus leucogenys	ENSNLEG00000006466	2 retrocopies	retro_nleu_1631, retro_nleu_2590,
Otolemur garnettii	ENSOGAG00000001860	1 retrocopy	retro_ogar_3308,
Pongo abelii	ENSPPYG00000015167	1 retrocopy	retro_pabe_329,
Pan troglodytes	ENSPTRG00000023618	2 retrocopies	retro_ptro_294, retro_ptro_3035,
Rattus norvegicus	ENSRNOG00000014188	3 retrocopies	retro_rnor_2309, retro_rnor_845, retro_rnor_846,
Sorex araneus	ENSSARG00000003780	1 retrocopy	retro_sara_168,
Ictidomys tridecemlineatus	ENSSTOG00000024763	3 retrocopies	retro_itri_1085 , retro_itri_1372, retro_itri_715,
Tupaia belangeri	ENSTBEG00000017224	7 retrocopies	retro_tbel_168, retro_tbel_2196, retro_tbel_2345, retro_tbel_2474, retro_tbel_3235, retro_tbel_3987, retro_tbel_4393,
Tarsius syrichta	ENSTSYG00000008284	1 retrocopy	retro_tsyr_686,