RetrogeneDB ID: retro_itri_83

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393333.1:1211761..1212271(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020213
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TIMM17B
• Ensembl ID: ENSSTOG00000014173
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17 homolog B (yeast) [Source:HGNC Symbol;Acc:17310]

Sequence

>retro_itri_83
ATGGAGGAATATGCCAGAGAGCCTTGCCCCTGGCGAATTGTGGATGACTGTGGTGGGGCCTTTACGATGGGTACCATAGG
TGGTGGTGTCTTTCAAGCAATCAAAGGTTTTCAAAATTCTCCAGTGGGAGTAAACCACAGACTACGAGGGAGTTTGACAG
CAATTAGAACCAGGGCTTCACAATTGGGAGGTAGTTTTGTGGTTTGGGGAGGCCTGTTCTCTATGATTGACTGTAGTATG
GTTCAAGTCAGAGGAAAAGAAGATCCCTGGAACTCCATCACTAATGGTGCCTTAACAGGAGCTATACTGGCAGCAAGAAA
TGGTCCAGTGGCCATGGTTGGGTCAGCTGCAATGGGTGGCATTCTCCTAGCTTTAATTGAAGGAGCTGGCATCTTGTTGA
CAAGATTTGCCTCTACACAGTTTCCCCATGGTCCTCCCTTTGCTGAAGACCCCTCCCAGTTGCCTTCCATTCAGTTACCA
TCCTCACCTTTTGGATACTATCGACAATAA

Alignment

ORF - retro_itri_83 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.51 %
• Parental protein coverage: 91.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PWRIVDDCGGAFTMGVIGGGVFQAIKGFRNAPVGIQHRLRSSINTVRIHAPQIGGSFAVWGFLFSTVDCG
          PWRIVDDCGGAFTMG.IGGGVFQAIKGF.N.PVG..HRLR.S....R..A.Q.GGSF.VWG.LFS..DC.
Retrocopy PWRIVDDCGGAFTMGTIGGGVFQAIKGFQNSPVGVNHRLRGSLTAIRTRASQLGGSFVVWGGLFSMIDCS

Parental  LVQLRGREDPWNSITSGAVTGAVLAARSGPLAMVGSAMMGGILLALVEGVSILLTRFTSRQFRNVPPLLE
          .VQ.RG.EDPWNSIT.GA.TGA.LAAR.GP.AMVGSA.MGGILLAL.EG..ILLTRF.S.QF...PP..E
Retrocopy MVQVRGKEDPWNSITNGALTGAILAARNGPVAMVGSAAMGGILLALIEGAGILLTRFASTQFPHGPPFAE

Parental  DPSQLSPKEDTPDTDF
          DPSQL.P....P...F
Retrocopy DPSQL-PSIQLPSSPF

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_83 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_83 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012474	1 retrocopy	retro_amel_717,
Bos taurus	ENSBTAG00000018496	4 retrocopies	retro_btau_1022, retro_btau_1550, retro_btau_1552, retro_btau_882,
Cavia porcellus	ENSCPOG00000008768	2 retrocopies	retro_cpor_867, retro_cpor_893,
Dasypus novemcinctus	ENSDNOG00000025897	2 retrocopies	retro_dnov_2282, retro_dnov_2406,
Felis catus	ENSFCAG00000002569	2 retrocopies	retro_fcat_1429, retro_fcat_1654,
Gorilla gorilla	ENSGGOG00000011427	1 retrocopy	retro_ggor_779,
Macropus eugenii	ENSMEUG00000004174	1 retrocopy	retro_meug_2071,
Microcebus murinus	ENSMICG00000005971	3 retrocopies	retro_mmur_1128, retro_mmur_1272, retro_mmur_232,
Myotis lucifugus	ENSMLUG00000009148	1 retrocopy	retro_mluc_148,
Macaca mulatta	ENSMMUG00000004547	1 retrocopy	retro_mmul_796,
Mustela putorius furo	ENSMPUG00000013675	1 retrocopy	retro_mputfur_1232,
Mus musculus	ENSMUSG00000031158	1 retrocopy	retro_mmus_1509,
Nomascus leucogenys	ENSNLEG00000007902	1 retrocopy	retro_nleu_1616,
Oryctolagus cuniculus	ENSOCUG00000027418	2 retrocopies	retro_ocun_121, retro_ocun_1451,
Pteropus vampyrus	ENSPVAG00000007643	1 retrocopy	retro_pvam_470,
Ictidomys tridecemlineatus	ENSSTOG00000014173	1 retrocopy	retro_itri_83 ,
Tarsius syrichta	ENSTSYG00000010396	2 retrocopies	retro_tsyr_1132, retro_tsyr_1703,
Vicugna pacos	ENSVPAG00000009578	1 retrocopy	retro_vpac_92,