RetrogeneDB ID: retro_itri_1380

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393466.1:3897098..3897510(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSSTOG00000006322
• Aliases: None
• Description: ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]

Sequence

>retro_itri_1380
GAGTGTTGTACTAGCAAAACAAGGATCATTGATGTTGTCTACAATGCATCCAGTAATGAGCTGGTCCACACCAAGACCCT
CATGAAGAACTGCAGCATGCTCATTGAGAGCACACCATACCAACAGTGGTACAAGTCCCACTACATACCGCCCCTGGGCT
GCAAGAAGGGGGCCAAGCTGACTTCTGAGGAGGAAGAAATTTTAAACAAAGACTGATCAAAGAAAATTCAAAAGAAATAC
GATGAAAGGAAGAAAAATGCTAAAATCAACACTCTTCTGGAAGAGCAGTCAGGGCAAGCTTCTTGCCTGCATTGCATTAA
GATCAGGACAGTGTAGCCAAGCAGATGGTTATGTGCTAGAAGGCAAGAAGCTGGAGTTCTATTTGAGGAAAATCAAAGCT
GGGAAAGGTAAA

Alignment

ORF - retro_itri_1380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.71 %
• Parental protein coverage: 66.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNK
          ECCT.KTRIIDVVYNAS.NELV.TKTL.KNC..LI.STPY.QWY.SHY..PLG.KKGAKLT.EEEEILNK
Retrocopy ECCTSKTRIIDVVYNASSNELVHTKTLMKNCSMLIESTPYQQWYKSHYIPPLGCKKGAKLTSEEEEILNK

Parental  KRS-KKIQKKYDERKKNAKISTLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
          ..S..K.........K..K.STL......QGKLLACIA.R.GQC..ADGYVLEGK.LEFYLRKIKA.KGK
Retrocopy D*S>RKFKRNTMKGRKMLK-STLFWKS-SQGKLLACIALRSGQCSQADGYVLEGKKLEFYLRKIKAGKGK

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_1380 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1380 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 91 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
Choloepus hoffmanni	ENSCHOG00000008785	10 retrocopies	retro_chof_1197, retro_chof_1258, retro_chof_1466, retro_chof_1638, retro_chof_2066, retro_chof_2617, retro_chof_2633, retro_chof_274, retro_chof_331, retro_chof_951,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Homo sapiens	ENSG00000142937	8 retrocopies	retro_hsap_1467, retro_hsap_1536, retro_hsap_1942, retro_hsap_2034, retro_hsap_2791, retro_hsap_3158, retro_hsap_3410, retro_hsap_635,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Monodelphis domestica	ENSMODG00000028389	1 retrocopy	retro_mdom_998,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,
Sorex araneus	ENSSARG00000000899	1 retrocopy	retro_sara_462,
Ictidomys tridecemlineatus	ENSSTOG00000006322	3 retrocopies	retro_itri_1337, retro_itri_1380 , retro_itri_750,
Tursiops truncatus	ENSTTRG00000003388	4 retrocopies	retro_ttru_1839, retro_ttru_282, retro_ttru_300, retro_ttru_344,