RetrogeneDB ID: retro_itri_539

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393300.1:796856..797435(+)
• Located in intron of: ENSSTOG00000002530

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM20B
• Ensembl ID: ENSSTOG00000005086
• Aliases: None
• Description: family with sequence similarity 20, member B [Source:HGNC Symbol;Acc:23017]

Sequence

>retro_itri_539
ATGGCCACCAAGAAAATCATTAAAGCCGATGTAGGTTATAAAGGGACAGAGCTGAAAGCCTTACTGATACTTGAAGGAGG
ACAGAAAGTTGTCTTCAAACCTAAGCAGTGTAGGCGAGACTATGTGGTGGAAGGGGAGCCATATGCTGGTTATGATAGAC
ACAATGCAGAGGTAGCAGCCTTTCATTTAGACAGGATTCGGGGTTTCTGCCAAGCCTCCTTGGTGGTTGGCAGTTTGTTA
ATCTACGGACAGATCAAGCCTGTTGCTGCGGAGCAGCTGTTGAGCACCTTCCTAGCTATAGGAAACAATACTTGTTTCTA
TGGGAAGTGCTACTACTGCTGAGAAACAGAGCCAGTTTGTGAAGATGGAGACACAATGGAGGGATCTGTGATGCTTTGGC
TTCCAAATGTGTGGCCTCTGCAGAAACACTGACACTCCTGGAGCAGGACTTACCAAGAAGGCAAATTGGCCAGGTGGGAG
TATGATGAGAGCTACTGTGTTACTGTGAAGAAAACGTCCCCATATGACTCAGACCCACGCCTCTTGGACATCATTGACAC
CTCTGTCTTTGATTACCTA

Alignment

ORF - retro_itri_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.54 %
• Parental protein coverage: 60.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATKKIIKADVGYKGTQLKALLILEGGQKVVFKPKRYSRDYVVEGEPYAGYDRHNAEVAAFHLDRILGFR
          MATKKIIKADVGYKGT.LKALLILEGGQKVVFKPK...RDYVVEGEPYAGYDRHNAEVAAFHLDRI.GF.
Retrocopy MATKKIIKADVGYKGTELKALLILEGGQKVVFKPKQCRRDYVVEGEPYAGYDRHNAEVAAFHLDRIRGFC

Parental  RAPLVVGRFVNLRTEIKPVATEQLLSTFLAVGNNTCFYGKCYYCRETEPACADGDTMEGSVTLWLPDVWP
          .A.LVVG........IKPVA.EQLLSTFLA.GNNTCFYGKCYYC.ETEP.C.DGDTMEGSV.LWLP.VWP
Retrocopy QASLVVGSLL-IYGQIKPVAAEQLLSTFLAIGNNTCFYGKCYYC*ETEPVCEDGDTMEGSVMLWLPNVWP

Parental  LQKHRHPWGRTYREGKLARWEYDESYCDAVKKTSPYDSGPRLLDIIDTSVFDYL
          LQKH.H.W.RTY.EGKLARWEYDESYC..VKKTSPYDS.PRLLDIIDTSVFDYL
Retrocopy LQKH*HSWSRTYQEGKLARWEYDESYCVTVKKTSPYDSDPRLLDIIDTSVFDYL

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_539 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_539 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005236	6 retrocopies	retro_chof_1509, retro_chof_1926, retro_chof_2615, retro_chof_2629, retro_chof_799, retro_chof_868,
Dasypus novemcinctus	ENSDNOG00000006175	2 retrocopies	retro_dnov_1484, retro_dnov_2346,
Echinops telfairi	ENSETEG00000005651	1 retrocopy	retro_etel_1128,
Homo sapiens	ENSG00000116199	1 retrocopy	retro_hsap_2730,
Gorilla gorilla	ENSGGOG00000002484	1 retrocopy	retro_ggor_1899,
Macropus eugenii	ENSMEUG00000006654	1 retrocopy	retro_meug_414,
Macaca mulatta	ENSMMUG00000006260	1 retrocopy	retro_mmul_1533,
Nomascus leucogenys	ENSNLEG00000015580	1 retrocopy	retro_nleu_592,
Otolemur garnettii	ENSOGAG00000012751	1 retrocopy	retro_ogar_2800,
Pongo abelii	ENSPPYG00000000466	2 retrocopies	retro_pabe_2268, retro_pabe_2269,
Pan troglodytes	ENSPTRG00000001725	1 retrocopy	retro_ptro_1845,
Ictidomys tridecemlineatus	ENSSTOG00000005086	2 retrocopies	retro_itri_441, retro_itri_539 ,
Tarsius syrichta	ENSTSYG00000005482	3 retrocopies	retro_tsyr_2065, retro_tsyr_2124, retro_tsyr_89,