RetrogeneDB ID: retro_itri_488

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393295.1:14689715..14690368(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004475
• Aliases: None
• Description: None

Sequence

>retro_itri_488
GGCAGGGAGAGCTGGTATCAGAAGCCAGGCATGGGTTTGGATACTATCAATGATACTCTGCTACCAGAAGCATATGTCTA
CCACCTGCTGACGTTCTACTGCCGGAAACAGTCCTGCTATTTGAATTTGATTGAGCTCTTCCTGCAGAGTTCCTATCAAA
ATGAGATGGGGCAGATCCTGGACCTCATCCCAGTCCCCCAGGATAATGCGGATCTTGGAAGATACACTGAAAAGAGATAC
AAATCCATTGTCAAGTAAAGAGAACTTTGCACTATTTCTCCCTGCCTATCACTGCTGCCATGTTCATGGAAAGCATTAAT
GGGGAGAAGGAACATGCCAACGCCAAGAAGATCCTGATTGAGATGAGAGAGTTCTTTCAGATTCAGGATGATTACCTTGA
CCTCTTTGGCGACTCCAGTGTAACAAGAAAGGTTGGAACTGACATCTAAGACAACAAGTGAAACTGGATGGTGGTTCAGT
GTCTGCAATGGGCCACTCCAGAACATCGCCAGATCTTACAGGAGAATTAGGGGCAGAAGGACACCAAGAAGGTGGCCCAG
GTGAGGGCACTATATGAGAAGATGAATCTACCATCTTTGTTCTCGAAGTATGAAGAAAACAGTTACAGCTACCTTATGAG
TCTCATTTAGCAA

Alignment

ORF - retro_itri_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GQLCWYQKPGIGLDAINDCLLLEACIYRLLKFYCRDQPYYLNLIELFLQSSYQTEIGQTLDLITAPQGNV
          G...WYQKPG.GLD.IND.LL.EA..Y.LL.FYCR.Q..YLNLIELFLQSSYQ.E.GQ.LDLI..PQ.N.
Retrocopy GRESWYQKPGMGLDTINDTLLPEAYVYHLLTFYCRKQSCYLNLIELFLQSSYQNEMGQILDLIPVPQDNA

Parental  DLGRYTEKRYKSIVK-YKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILMQMGEFFQIQDDYLDLFGDP
          DLGRYTEKRYKSIVK..K.....F.LPI.AAM.M..I.GEKEHANAKKIL..M.EFFQIQDDYLDLFGD.
Retrocopy DLGRYTEKRYKSIVK<VKRTLHYFSLPITAAMFMESINGEKEHANAKKILIEMREFFQIQDDYLDLFGDS

Parental  SVTGKVGTDIQDNKCSWLVVQCLQRATPEQRQILQDNYGQKDAKKVAQVRALYEEMNLPAVFSKYEEDSY
          SVT.KVGTDI.DNK..W.VVQCLQ.ATPE.RQILQ.N.GQKD.KKVAQVRALYE.MNLP..FSKYEE.SY
Retrocopy SVTRKVGTDI*DNK*NWMVVQCLQWATPEHRQILQEN*GQKDTKKVAQVRALYEKMNLPSLFSKYEENSY

Parental  IHLMSLIEQ
          ..LMSLI.Q
Retrocopy SYLMSLI*Q

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_488 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_488 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 13 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030749	2 retrocopies	retro_cfam_1822, retro_cfam_1888,
Callithrix jacchus	ENSCJAG00000008364	11 retrocopies	retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011, retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi	ENSETEG00000001154	6 retrocopies	retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Homo sapiens	ENSG00000160752	6 retrocopies	retro_hsap_1519, retro_hsap_1558, retro_hsap_1560, retro_hsap_3871, retro_hsap_3872, retro_hsap_502,
Microcebus murinus	ENSMICG00000007468	1 retrocopy	retro_mmur_1148,
Macaca mulatta	ENSMMUG00000023144	3 retrocopies	retro_mmul_1190, retro_mmul_2152, retro_mmul_565,
Mus musculus	ENSMUSG00000059743	5 retrocopies	retro_mmus_1028, retro_mmus_1552, retro_mmus_2802, retro_mmus_3625, retro_mmus_590,
Nomascus leucogenys	ENSNLEG00000012099	6 retrocopies	retro_nleu_1486, retro_nleu_1727, retro_nleu_2301, retro_nleu_2405, retro_nleu_2595, retro_nleu_2692,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Pan troglodytes	ENSPTRG00000001422	9 retrocopies	retro_ptro_1028, retro_ptro_1048, retro_ptro_1049, retro_ptro_2637, retro_ptro_2638, retro_ptro_2639, retro_ptro_2940, retro_ptro_2995, retro_ptro_377,
Rattus norvegicus	ENSRNOG00000043377	3 retrocopies	retro_rnor_1175, retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus	ENSSTOG00000004475	1 retrocopy	retro_itri_488 ,
Tursiops truncatus	ENSTTRG00000013326	1 retrocopy	retro_ttru_689,