RetrogeneDB ID: retro_itri_1108

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393376.1:5966095..5966491(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023993
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011101
• Aliases: None
• Description: None

Sequence

>retro_itri_1108
AGAAAGCGTTGTGGTGGAAAGTAAGTTCTAGACACATCCAGAAGAGAACCCAGGAAGCAGCCTCCACCTCTGAGATTTCC
TTGGAAGCAGAACCTATAGAACTCGTGGAAACTGCTGGAGATGAAATCGTGGACCTCACCTGTGAGTCTTTAGAGCCTGT
GGTGGTGAACCTGACTCCCAATGACTCTGTTGTGATTGTTGACGAAGGAGAAGGCCCAAGAGGAATGCAGGAGGCTGCGA
CAAGACCATGCCAACAGTTGCGTGGTGGGCAGTGATGACGAGGAGTTGTCCAGGGACAGAGATGTGTATGGGACCACCCA
CACTCCCAGAAATGCCAGGGAGGAAAGGGCCACAGGGCTCAGACCCTCTGGTACTGTCAGTTGTCCCATCTGCATG

Alignment

ORF - retro_itri_1108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 70. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKRRGGT-VNSRQAQKRTREAASTPEISLEAEPIELVETAGDEIVDLTCESLEPVVVDLTHNDSIVIVDE
          RKR.GG..V.SR..QKRT.EAAST.EISLEAEPIELVETAGDEIVDLTCESLEPVVV.LT.NDS.VIVDE
Retrocopy RKRCGGK<VSSRHIQKRTQEAASTSEISLEAEPIELVETAGDEIVDLTCESLEPVVVNLTPNDSVVIVDE

Parental  -RRRPRRNA-RRLRQDHPDSCVVSSDDEELSRDRDVYVTTPTPRNARDEGATGLRPSGTVSCPICM
          .RRRP.RNA.RRLRQDH..SCVV.SDDEELSRDRDVY.TT.TPRNAR.E.ATGLRPSGTVSCPICM
Retrocopy <RRRPKRNA<RRLRQDHANSCVVGSDDEELSRDRDVYGTTHTPRNAREERATGLRPSGTVSCPICM

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_1108 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1108 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 22 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Dipodomys ordii	ENSDORG00000006675	2 retrocopies	retro_dord_347, retro_dord_411,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33,
Echinops telfairi	ENSETEG00000001683	3 retrocopies	retro_etel_469, retro_etel_626, retro_etel_627,
Felis catus	ENSFCAG00000004051	1 retrocopy	retro_fcat_897,
Homo sapiens	ENSG00000063978	1 retrocopy	retro_hsap_319,
Gorilla gorilla	ENSGGOG00000015149	2 retrocopies	retro_ggor_1144, retro_ggor_345,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Microcebus murinus	ENSMICG00000001767	1 retrocopy	retro_mmur_1265,
Myotis lucifugus	ENSMLUG00000005969	1 retrocopy	retro_mluc_1640,
Mus musculus	ENSMUSG00000029110	1 retrocopy	retro_mmus_522,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Otolemur garnettii	ENSOGAG00000010776	1 retrocopy	retro_ogar_2121,
Ochotona princeps	ENSOPRG00000004317	3 retrocopies	retro_opri_112, retro_opri_783, retro_opri_863,
Procavia capensis	ENSPCAG00000004528	1 retrocopy	retro_pcap_208,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Pteropus vampyrus	ENSPVAG00000017017	1 retrocopy	retro_pvam_167,
Sus scrofa	ENSSSCG00000008690	1 retrocopy	retro_sscr_181,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108 , retro_itri_171,
Tarsius syrichta	ENSTSYG00000011244	1 retrocopy	retro_tsyr_1606,