RetrogeneDB ID: retro_itri_1623

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393579.1:703749..703999(+)
• Located in intron of: ENSSTOG00000011590

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA38
• Ensembl ID: ENSSTOG00000009039
• Aliases: None
• Description: N(alpha)-acetyltransferase 38, NatC auxiliary subunit [Source:HGNC Symbol;Acc:20471]

Sequence

>retro_itri_1623
ACTGTTGCTGTCATTACTTCTGATGGGAGAAGGACTGTGGGAACACTGAAAGATTCCACCAGACCATTAATTTGATCTTG
GATGAAAGCCACGAACAACTTACCCAGCTCTTCGCAGGGAGCAGGACGAGTGGTACTAGCCTATATGTTGTAAGAGGTGA
CAATGCTGCTGTCACTGGAGAAACGGGTGAAGAGACAGATTCTGCCCTGGACCTGGGGAATGTTCCAGCAGAACTCTAAA
CTCTGCAGCA

Alignment

ORF - retro_itri_1623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TVAVITSDGRMIVGTLKG-FDQTINLILDESHERVF-SSSQGVEQVVL-GLYIVRGDNVAVIGEIDEETD
          TVAVITSDGR..VGTLK..F.QTINLILDESHE....SSSQG...VVL..LY.VRGDN.AV.GE..EETD
Retrocopy TVAVITSDGRRTVGTLKD<FHQTINLILDESHEQLT>SSSQGAGRVVL<SLYVVRGDNAAVTGETGEETD

Parental  SALDLGNIRAE-PLNSVA
          SALDLGN..AE..LNS.A
Retrocopy SALDLGNVPAE<TLNSAA

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_1623 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1623 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001162	1 retrocopy	retro_amel_1716,
Echinops telfairi	ENSETEG00000011594	1 retrocopy	retro_etel_491,
Felis catus	ENSFCAG00000023642	1 retrocopy	retro_fcat_1993,
Myotis lucifugus	ENSMLUG00000006837	1 retrocopy	retro_mluc_161,
Macaca mulatta	ENSMMUG00000015822	1 retrocopy	retro_mmul_2010,
Mustela putorius furo	ENSMPUG00000007100	1 retrocopy	retro_mputfur_1440,
Oryctolagus cuniculus	ENSOCUG00000017359	2 retrocopies	retro_ocun_1715, retro_ocun_954,
Otolemur garnettii	ENSOGAG00000013377	1 retrocopy	retro_ogar_1071,
Ochotona princeps	ENSOPRG00000014809	2 retrocopies	retro_opri_1033, retro_opri_227,
Sarcophilus harrisii	ENSSHAG00000018435	1 retrocopy	retro_shar_535,
Ictidomys tridecemlineatus	ENSSTOG00000009039	3 retrocopies	retro_itri_1623 , retro_itri_364, retro_itri_679,