RetrogeneDB ID: retro_itri_196

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:48858670..48859021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000020783
• Aliases: None
• Description: None

Sequence

>retro_itri_196
CAAGAAGATGCCAGAAAGTAGCCCAAGAAAGACAGGAAGCCAGTAAGCAAATCTGGGGGCAAAGCAAACACAAGAAGTGA
TCCAAAGGCAAAGTTCGGGACAAACTCACCAATCTAGCCTTGTTTGACAAAGCTACTTAGGACGAACTTTGTATGGAAGT
TCTCAACTACGACCTCATAACCCCAGCTGTGGTCTCTGAGAGACGGAAGATTCGAGGTTCCCTGGCCAGAGCAGCCCTTG
AGGAGTTCCCCAGGAAAGGACTTAACCAACCTGATTTCAAAGGACAGAGCTCAAGTGATTTATACCACAAATACCAAGGG
TGGAGATGCCCCAGATTCTGGTGAAGATGCC

Alignment

ORF - retro_itri_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.95 %
• Parental protein coverage: 94.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKDAGKSAKKDKDPVNKSGGKA-KKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERL
          ..DA.K..KKD..PV.KSGGKA.K.KK.SKGKVRDKL.NL.LFDKAT.D.LC.EV.NY.LITPAVVSER.
Retrocopy QEDARK*PKKDRKPVSKSGGKA<KHKK*SKGKVRDKLTNLALFDKAT*DELCMEVLNYDLITPAVVSERR

Parental  KIRGSLARAALQELLSKG-LIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
          KIRGSLARAAL.E...KG.L..L.SK.RAQVIYT.NTKGGDAP..GEDA
Retrocopy KIRGSLARAALEEFPRKG>LTNLISKDRAQVIYTTNTKGGDAPDSGEDA

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_196 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_196 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 9 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012395	3 retrocopies	retro_cfam_500, retro_cfam_680, retro_cfam_984,
Felis catus	ENSFCAG00000001151	3 retrocopies	retro_fcat_1792, retro_fcat_601, retro_fcat_903,
Latimeria chalumnae	ENSLACG00000017531	4 retrocopies	retro_lcha_101, retro_lcha_118, retro_lcha_50, retro_lcha_72,
Macropus eugenii	ENSMEUG00000014185	3 retrocopies	retro_meug_1181, retro_meug_1562, retro_meug_174,
Microcebus murinus	ENSMICG00000002687	8 retrocopies	retro_mmur_1023, retro_mmur_1514, retro_mmur_229, retro_mmur_308, retro_mmur_387, retro_mmur_425, retro_mmur_485, retro_mmur_688,
Macaca mulatta	ENSMMUG00000016894	2 retrocopies	retro_mmul_137, retro_mmul_71,
Ochotona princeps	ENSOPRG00000016194	9 retrocopies	retro_opri_1099, retro_opri_1204, retro_opri_256, retro_opri_320, retro_opri_393, retro_opri_493, retro_opri_64, retro_opri_854, retro_opri_873,
Ictidomys tridecemlineatus	ENSSTOG00000020783	3 retrocopies	retro_itri_1491, retro_itri_196 , retro_itri_87,
Vicugna pacos	ENSVPAG00000000266	4 retrocopies	retro_vpac_106, retro_vpac_118, retro_vpac_337, retro_vpac_546,