RetrogeneDB ID: retro_itri_596

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393305.1:4164706..4165014(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000022124
• Aliases: None
• Description: None

Sequence

>retro_itri_596
AAGCAATTGTTTCACAGCTCTCCTGCTACAGTGGAAAGTTTTTTAAGTTGGAAGGACAAGTCTGAGGCAGAACTCTTGAA
AATTAAAAAGCAATGGAAGAAAGAAGAACAAGCAGGGAAAAAATAAATTTAGTGGGAAACAGCTACTTGATACATTCTAA
TGTCAACACATCTGATATTCAGTTCTTGGAGGATGCTGGAAACAATGGGGAGGTAGATGAGTCTTTGTTTCATAAAAGGG
ATGATTTGAAGCAGAAGAATAATGAGGACAATCTGAACTACACTCCTGCTGCCCCAGAGAGTGACTCT

Alignment

ORF - retro_itri_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.72 %
• Parental protein coverage: 98.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQLFHGTSVSIENFLSWEAKFDVELLKIKKKKQLKEEEQA-EKINVSRKQLFETDHNLDTSDIQFLEDAG
          KQLFH......E.FLSW..K...ELLKIKK....KEE....EKIN...........N..TSDIQFLEDAG
Retrocopy KQLFHSSPATVESFLSWKDKSEAELLKIKKQWK-KEEQAG<EKINLVGNS-YLIHSNVNTSDIQFLEDAG

Parental  NNVEVDESLFQEMDDLELEDDEDDPDYNPADPGSDS
          NN.EVDESLF...DDL.....ED...Y.PA.P.SDS
Retrocopy NNGEVDESLFHKRDDLKQKNNEDNLNYTPAAPESDS

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_596 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_596 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Dasypus novemcinctus	ENSDNOG00000007516	1 retrocopy	retro_dnov_2467,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596 ,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,