RetrogeneDB ID: retro_itri_1656

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393611.1:459035..459396(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA20
• Ensembl ID: ENSSTOG00000014733
• Aliases: None
• Description: N(alpha)-acetyltransferase 20, NatB catalytic subunit [Source:HGNC Symbol;Acc:15908]

Sequence

>retro_itri_1656
ATTATGGGTAAAGCAGAAGGCTCAGTAGCCAGGGCAGAATGGCATGGGCATGTCACAGCTCTGTCTGATGCCCCTGAATT
TTAACACCTTGATTTGGCTGCTAAACTTAGAGTTATTAGAGGATATTTCAGAAAGAAGAAGTGGATTTTTTTTTGGTTGA
TCTCTTTGTAAGAGTATAACCAAGTTGCAGTCAACATGTACAAGCAGTTGGCCTACAGTGTGTACAGGACAGTTGTTAGA
GTACTATTCAGCCAGCAATGGGGAGCCCGATGAGGATGCTTATGATATGAGTAAGGCACTTTCCAGGGATACCAAACAGA
AATCTGTCACACCATTACCTCATTCTGTGAGGCCTGAAGAC

Alignment

ORF - retro_itri_1656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.42 %
• Parental protein coverage: 63.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VMGKAEGSVAREEWHGHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQL
          .MGKAEGSVAR.EWHGHVTALS.APEF..L.LAAKL..........K............NQVAVNMYKQL
Retrocopy IMGKAEGSVARAEWHGHVTALSDAPEF*HLDLAAKLRVIRGYFRKKKWXXXXLISL*EYNQVAVNMYKQL

Parental  GYSVYRTVI-EYYSASNGEPDEDAYDMRKALSRDTEKKSIIPLPHPVRPED
          .YSVYRTV..EYYSASNGEPDEDAYDM.KALSRDT..KS..PLPH.VRPED
Retrocopy AYSVYRTVV>EYYSASNGEPDEDAYDMSKALSRDTKQKSVTPLPHSVRPED

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_1656 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1656 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001144	1 retrocopy	retro_btau_899,
Canis familiaris	ENSCAFG00000032025	1 retrocopy	retro_cfam_768,
Callithrix jacchus	ENSCJAG00000005377	4 retrocopies	retro_cjac_1099, retro_cjac_1629, retro_cjac_2984, retro_cjac_439,
Gorilla gorilla	ENSGGOG00000004247	1 retrocopy	retro_ggor_374,
Microcebus murinus	ENSMICG00000006044	1 retrocopy	retro_mmur_540,
Macaca mulatta	ENSMMUG00000007708	1 retrocopy	retro_mmul_479,
Mustela putorius furo	ENSMPUG00000001228	2 retrocopies	retro_mputfur_1495, retro_mputfur_321,
Mus musculus	ENSMUSG00000002728	3 retrocopies	retro_mmus_1228, retro_mmus_3146, retro_mmus_3257,
Nomascus leucogenys	ENSNLEG00000009855	1 retrocopy	retro_nleu_2267,
Oryctolagus cuniculus	ENSOCUG00000015481	1 retrocopy	retro_ocun_1331,
Otolemur garnettii	ENSOGAG00000011542	1 retrocopy	retro_ogar_2007,
Pongo abelii	ENSPPYG00000010746	1 retrocopy	retro_pabe_342,
Pan troglodytes	ENSPTRG00000013299	1 retrocopy	retro_ptro_284,
Ictidomys tridecemlineatus	ENSSTOG00000014733	1 retrocopy	retro_itri_1656 ,
Tupaia belangeri	ENSTBEG00000000969	1 retrocopy	retro_tbel_567,