RetrogeneDB ID: retro_itri_1039

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393361.1:3323851..3324152(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS36
• Ensembl ID: ENSSTOG00000021863
• Aliases: None
• Description: mitochondrial ribosomal protein S36 [Source:HGNC Symbol;Acc:16631]

Sequence

>retro_itri_1039
ATGGGCAGCAAGATGGTTTCTTCCAGCAGAGTTATTTAGGCAGTCAATTCACATAATATGGTAATGTTTGCCTGACAGGA
GAGACAACCCTAAATTCAGTTATCAGAAGCTTTGAGATCAGCAAGGCTACCATACCACTCTTTGTAATTTAACAGCATCT
TAAGAAAGGTAAATCACCAGATTGGGGAAGCATCAAGATCAACCAGACACTACAGAAATAATAAAAACATTACTTCAGAA
GTACAAAAGGAAAGCCATATCTCAGGAAGTAATAAAATTTATCCAAAATTGAGGTACAGAA

Alignment

ORF - retro_itri_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGSKMASASRVVQVVKPHTPLIRF-PDRRNNPKLS-VTEGLRSAGLPSHSP-VISQHSKGNKSPD-LLMH
          MGSKM.S.SRV...V..H.....F.PDRR.NPK.S...E.LRSA.LP.HS..VI.QH.K..KSPD.L..H
Retrocopy MGSKMVSSSRVI*AVNSHN-MVMF>PDRRDNPKFS<LSEALRSARLPYHSL<VI*QHLKKGKSPD<LGKH

Parental  HGPPDTAEIIKTLPQKYRRKPVSQEEMEFIQRGGPE
          ...PDT.EIIKTL.QKY.RK..SQE...FIQ..G.E
Retrocopy QDQPDTTEIIKTLLQKYKRKAISQEVIKFIQN*GTE

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_1039 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1039 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 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003161	2 retrocopies	retro_amel_1838, retro_amel_565,
Callithrix jacchus	ENSCJAG00000016092	2 retrocopies	retro_cjac_3202, retro_cjac_45,
Dipodomys ordii	ENSDORG00000007063	1 retrocopy	retro_dord_110,
Echinops telfairi	ENSETEG00000019493	2 retrocopies	retro_etel_1624, retro_etel_625,
Felis catus	ENSFCAG00000031782	1 retrocopy	retro_fcat_724,
Homo sapiens	ENSG00000134056	2 retrocopies	retro_hsap_2750, retro_hsap_823,
Loxodonta africana	ENSLAFG00000007932	2 retrocopies	retro_lafr_1243, retro_lafr_598,
Monodelphis domestica	ENSMODG00000019701	1 retrocopy	retro_mdom_1559,
Mus musculus	ENSMUSG00000061474	4 retrocopies	retro_mmus_105, retro_mmus_123, retro_mmus_3223, retro_mmus_753,
Nomascus leucogenys	ENSNLEG00000004071	4 retrocopies	retro_nleu_1545, retro_nleu_196, retro_nleu_2243, retro_nleu_257,
Oryctolagus cuniculus	ENSOCUG00000005261	2 retrocopies	retro_ocun_1057, retro_ocun_1109,
Otolemur garnettii	ENSOGAG00000024260	9 retrocopies	retro_ogar_1166, retro_ogar_1716, retro_ogar_2238, retro_ogar_2363, retro_ogar_2629, retro_ogar_3382, retro_ogar_711, retro_ogar_790, retro_ogar_869,
Ochotona princeps	ENSOPRG00000011392	1 retrocopy	retro_opri_587,
Pongo abelii	ENSPPYG00000015524	3 retrocopies	retro_pabe_2219, retro_pabe_735, retro_pabe_917,
Pan troglodytes	ENSPTRG00000016944	4 retrocopies	retro_ptro_1858, retro_ptro_2038, retro_ptro_573, retro_ptro_690,
Pteropus vampyrus	ENSPVAG00000010843	1 retrocopy	retro_pvam_174,
Rattus norvegicus	ENSRNOG00000048862	2 retrocopies	retro_rnor_1792, retro_rnor_2014,
Ictidomys tridecemlineatus	ENSSTOG00000021863	2 retrocopies	retro_itri_1039 , retro_itri_938,
Tupaia belangeri	ENSTBEG00000012048	22 retrocopies	retro_tbel_1313, retro_tbel_1494, retro_tbel_1527, retro_tbel_224, retro_tbel_2404, retro_tbel_2661, retro_tbel_2755, retro_tbel_2762, retro_tbel_2924, retro_tbel_2934, retro_tbel_3239, retro_tbel_3240, retro_tbel_359, retro_tbel_3891, retro_tbel_3893, retro_tbel_3941, retro_tbel_4124, retro_tbel_4429, retro_tbel_4515, retro_tbel_4543, retro_tbel_4592, retro_tbel_702,