RetrogeneDB ID: retro_itri_1419

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393481.1:3124071..3124598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000027831
• Aliases: None
• Description: None

Sequence

>retro_itri_1419
GCACAAAAGCACATGCAGCTAAATATATGTTTTCCATCTTAATGAAGAACATTACTTCATATCAACTTCTTGGCACTGTT
ATTTATAGTTTTGCTCTGGGTAAAACCAATCACCAAAGACTACATTATGAACCCACCATTGGGTAAAGAAAGTGTCCCTT
TAATGACAAAAGCTACATTTGATGCTCTACTACTCTGGTTAATAATCCTGCTGTGTGTTTTGAGATTGGCCATGATGCGT
AGTCACCTGCAAGCATATTTAAACTTAGCCCAGAAGTGTGTGGATCAGATGAAGAAAGAAGCAGGACAAATAAGTATAGT
TGAGCCACAGAAATGATGGCTCGAGTCTTTTATTACCTTTGTGTCATTGCGCTGCAGTATATGGCACCTCTGGTAATGCT
GCTTCATACAGCTCTGCTTTTGAAAATACTAGATGATCATTCCTGGGGCATTTATCCAGAATCTGTCTCTACCTTACCAG
TGGATAATAGTCTACACTCCATTTCTGTTTACTCTGAATTACCTACC

Alignment

ORF - retro_itri_1419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.15 %
• Parental protein coverage: 50.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQMHLDALNLATEKITQTLLHINFLAPLFMVLLWVKPITKDYIMNPPLGKESVPLMTEATFDTLRLWLII
          AQ.H...LN........TLLHINFLA.LF.VLLWVKPITKDYIMNPPLGKESVPLMT.ATFD.L.LWLII
Retrocopy AQKHMQ-LNICFPS**RTLLHINFLALLFIVLLWVKPITKDYIMNPPLGKESVPLMTKATFDALLLWLII

Parental  LLCALRLAMMRSHLQAYLNLAQKCVDQMKKEAGRISTVELQK-MVARVFYYLCVIALQYVAPLVMLLHTT
          LLC.LRLAMMRSHLQAYLNLAQKCVDQMKKEAG.IS.VE.QK.M.ARVFYYLCVIALQY.APLVMLLHT.
Retrocopy LLCVLRLAMMRSHLQAYLNLAQKCVDQMKKEAGQISIVEPQK<MMARVFYYLCVIALQYMAPLVMLLHTA

Parental  LLLKTLGNHSWGIYPESVSTLPVDNSLHSNSVYSELPS
          LLLK.L..HSWGIYPESVSTLPVDNSLHS.SVYSELP.
Retrocopy LLLKILDDHSWGIYPESVSTLPVDNSLHSISVYSELPT

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_1419 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1419 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010857	1 retrocopy	retro_cjac_2671,
Homo sapiens	ENSG00000164180	1 retrocopy	retro_hsap_560,
Gorilla gorilla	ENSGGOG00000005684	1 retrocopy	retro_ggor_506,
Macaca mulatta	ENSMMUG00000009319	1 retrocopy	retro_mmul_719,
Nomascus leucogenys	ENSNLEG00000013645	1 retrocopy	retro_nleu_2224,
Pan troglodytes	ENSPTRG00000017064	1 retrocopy	retro_ptro_419,
Rattus norvegicus	ENSRNOG00000032414	1 retrocopy	retro_rnor_1023,
Ictidomys tridecemlineatus	ENSSTOG00000011141	1 retrocopy	retro_itri_1420,
Ictidomys tridecemlineatus	ENSSTOG00000027831	2 retrocopies	retro_itri_1419 , retro_itri_1787,