RetrogeneDB ID: retro_itri_479

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393294.1:13828952..13829530(+)
• Located in intron of: ENSSTOG00000010061

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL15
• Ensembl ID: ENSSTOG00000011153
• Aliases: None
• Description: ribosomal protein L15 [Source:HGNC Symbol;Acc:10306]

Sequence

>retro_itri_479
ATGGGCGCATACAAGTACACCCAGGAGCTATGAAGGAATAAGCAGCTGGATATATACACTTTCTTCTGAGGGTCCACTGC
CAGCAGTACTGCCAGCTTGCTGTGCTCCACAAGGCTCCCCACCCCACTCGGCTGGATAAAGTGCGCAGACTGGGATACAG
GGCTAAGCAAGTTTATGTCATATACAGGATCGTCTGTACCGTGGTGGCCGCAAACGCCCACTTCCTAAGGGTGCCACCTA
TAGCAAGCCTGTCCATCATGGCGTTAACTAGCTAAAGTTTGCCCGAAGTCTTCAGTCTGTTGCTGAGGATTGAGCTGGAC
ACTACTGTGGGTCTCTGAGAGTCCTGAATTCTTACTGGGTTGGTGAAGATTCCACATAGAAATTCTTCAAGGTTATCCTC
ATTGATCCATTCCACAAAGCTATTAGAACAAATCCCAACACTCAGTGAATCACCAAACTAGTCCACAAGCACAGGGAGAA
GCACAGCCTAACATGTGCAGGCCACAAGTTCCTTCCTATTGGTGGTTCTCGCGGGTGCAGCTTGGAGAAGATGCAATACT
CTCCAGCTACACCATTAC

Alignment

ORF - retro_itri_479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGAYKYIQELWRKKQSDV-MRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRI-RVRR
          MGAYKY.QEL.R.KQ.D....FLLRV.C.QY.QL..LH.AP.PTR.DK.RRLGY.AKQ.YVIYRI.R..R
Retrocopy MGAYKYTQEL*RNKQLDI<IHFLLRVHCQQYCQLAVLHKAPHPTRLDKVRRLGYRAKQVYVIYRI<RLYR

Parental  GGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPF
          GGRKRP.PKGATY.KPVHHGVN.LKFARSLQSVAE..AG..CG.LRVLNSYWVGEDST.KFF.VILIDPF
Retrocopy GGRKRPLPKGATYSKPVHHGVN*LKFARSLQSVAED*AGHYCGSLRVLNSYWVGEDST*KFFKVILIDPF

Parental  HKAIRRNPDTQWITKPVHKHRESRGLG-KGHKFHHTIGGSR-RAAWRRRNTLQLHRY
          HKAIR.NP.TQ.ITK.VHKHRE...L...GHKF...IGGSR..AAWRR.NTLQLH.Y
Retrocopy HKAIRTNPNTQ*ITKLVHKHREKHSLTCAGHKF-LPIGGSR>GAAWRRCNTLQLHHY

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_479 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_479 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 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033080	2 retrocopies	retro_btau_152, retro_btau_201,
Cavia porcellus	ENSCPOG00000002253	4 retrocopies	retro_cpor_620, retro_cpor_807, retro_cpor_900, retro_cpor_978,
Felis catus	ENSFCAG00000026237	6 retrocopies	retro_fcat_1820, retro_fcat_285, retro_fcat_306, retro_fcat_610, retro_fcat_930, retro_fcat_985,
Gorilla gorilla	ENSGGOG00000024274	13 retrocopies	retro_ggor_1327, retro_ggor_1611, retro_ggor_1716, retro_ggor_1989, retro_ggor_2029, retro_ggor_2125, retro_ggor_2314, retro_ggor_2473, retro_ggor_39, retro_ggor_524, retro_ggor_552, retro_ggor_654, retro_ggor_771,
Myotis lucifugus	ENSMLUG00000013809	15 retrocopies	retro_mluc_1357, retro_mluc_1709, retro_mluc_1720, retro_mluc_2052, retro_mluc_2142, retro_mluc_2454, retro_mluc_425, retro_mluc_623, retro_mluc_701, retro_mluc_714, retro_mluc_748, retro_mluc_749, retro_mluc_907, retro_mluc_943, retro_mluc_99,
Macaca mulatta	ENSMMUG00000006353	1 retrocopy	retro_mmul_209,
Monodelphis domestica	ENSMODG00000014880	3 retrocopies	retro_mdom_1315, retro_mdom_1803, retro_mdom_918,
Mustela putorius furo	ENSMPUG00000012148	7 retrocopies	retro_mputfur_1011, retro_mputfur_1252, retro_mputfur_1291, retro_mputfur_314, retro_mputfur_346, retro_mputfur_658, retro_mputfur_669,
Mus musculus	ENSMUSG00000012405	2 retrocopies	retro_mmus_118, retro_mmus_8,
Oryctolagus cuniculus	ENSOCUG00000010961	2 retrocopies	retro_ocun_215, retro_ocun_228,
Otolemur garnettii	ENSOGAG00000013056	13 retrocopies	retro_ogar_1066, retro_ogar_1129, retro_ogar_1182, retro_ogar_1453, retro_ogar_1483, retro_ogar_1629, retro_ogar_1809, retro_ogar_2378, retro_ogar_270, retro_ogar_3058, retro_ogar_3096, retro_ogar_3349, retro_ogar_903,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Rattus norvegicus	ENSRNOG00000008140	17 retrocopies	retro_rnor_1046, retro_rnor_1409, retro_rnor_1497, retro_rnor_1685, retro_rnor_1690, retro_rnor_1785, retro_rnor_2042, retro_rnor_2249, retro_rnor_2313, retro_rnor_2451, retro_rnor_2473, retro_rnor_2786, retro_rnor_2997, retro_rnor_428, retro_rnor_66, retro_rnor_710, retro_rnor_844,
Sus scrofa	ENSSSCG00000028079	5 retrocopies	retro_sscr_1219, retro_sscr_1225, retro_sscr_448, retro_sscr_968, retro_sscr_997,
Ictidomys tridecemlineatus	ENSSTOG00000011153	4 retrocopies	retro_itri_1445, retro_itri_1838, retro_itri_479 , retro_itri_785,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,