RetrogeneDB ID: retro_itri_1413

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393480.1:3219513..3220094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MARC2
• Ensembl ID: ENSSTOG00000006676
• Aliases: None
• Description: mitochondrial amidoxime reducing component 2 [Source:HGNC Symbol;Acc:26064]

Sequence

>retro_itri_1413
CAGACCCAGCCCACATGGCTCTGGGTTGCTGTCCGGAGTCTGGCCGGGAGGCACTGGGGACCATCGCTTGGCATCTCTCA
GGACCCAGGCCGTGACTGCAGCAGGTGAGCACCGTGGCCCAGATCTCCATCTACCTGATCAAGTCCTCCAAGGGGGTGCA
GGTCAATGAGGCCAAGTGCACCACCATGGGACTGCGCTGTGTCCACTTGTGAGACAGGTTTTGGCTGGTGATCAAGGAAG
ATGGATACATGGTCACTGCCCAGCAGGAGACTTGTCTTGTGCTGGTCTCTATCACTTACGAGAGCAACTGCCTGATACTC
TAGGCTCCCAACATGGAACAGCTGGTTTTGCCTGTCAAGCAGCCTTCTTCAAACCCACTCAAGGACTGCAGGCTATTTGG
CCTTGACATTAAAGGCAGAGATTGTGTGTCTGAGACCACTTAGTAGTTCACCAACTACTTGAAAACAGAAGCATACAGGT
TGGTTCAATTTGAAACAAGCGTGAAGGGAAGAGCATCAAAGAAAATTTTCCTTTTTGTACAGAATTACCAGGTGGCTTAT
CCAGACTGAAGCCCAATCTTG

Alignment

ORF - retro_itri_1413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.16 %
• Parental protein coverage: 58.86 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTRPSWLGVAALSLAA-VALGTVAWRHARPRRRRRLQQVGTVAQISIYPIKSCKGVQVNEAECTTMGLRC
          QT.P.WL.VA..SLA...ALGT.AW....P..R..LQQV.TVAQISIY.IKS.KGVQVNEA.CTTMGLRC
Retrocopy QTQPTWLWVAVRSLAG<EALGTIAWHLSGP--RP*LQQVSTVAQISIYLIKSSKGVQVNEAKCTTMGLRC

Parental  GNLRDRFWLVIKEDGHMITARQEPRLVLVSITYENNSLILKAPDMEQLVLPVKQPSSNPLHDCRLFGLDI
          ..L.DRFWLVIKEDG.M.TA.QE..LVLVSITYE.N.LIL.AP.MEQLVLPVKQPSSNPL.DCRLFGLDI
Retrocopy VHL*DRFWLVIKEDGYMVTAQQETCLVLVSITYESNCLIL*APNMEQLVLPVKQPSSNPLKDCRLFGLDI

Parental  KGRDCGDEVAQWFTNYLKTESYRLVQFETSMKGRASKKIFPSVQNYQVAYPDCSPIL
          KGRDC..E....FTNYLKTE.YRLVQFETS.KGRASKKIF..VQNYQVAYPD.SPIL
Retrocopy KGRDCVSETT**FTNYLKTEAYRLVQFETSVKGRASKKIFLFVQNYQVAYPD*SPIL

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_1413 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1413 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011332	1 retrocopy	retro_cfam_469,
Oryctolagus cuniculus	ENSOCUG00000013162	1 retrocopy	retro_ocun_1466,
Rattus norvegicus	ENSRNOG00000037850	1 retrocopy	retro_rnor_162,
Ictidomys tridecemlineatus	ENSSTOG00000006676	1 retrocopy	retro_itri_1413 ,