RetrogeneDB ID: retro_itri_1230

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393408.1:3231937..3232367(+)
• Located in intron of: ENSSTOG00000009266

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000002723
• Aliases: None
• Description: None

Sequence

>retro_itri_1230
CAAGAACAGTTCCAAGGCATGCACACCTTCTACTACCACAAGGCCCATGCCTGCATCATTGTGTTCAATATGCAGAGGGA
AGTCACCTATAAAAATCTAAACTTCTGGGAGACAGAGCTTGAGGAGTTCAGGCCAGAGATTCCATGCATTGTATGACCAG
CAAAACTGATATAGACATACATGTGACCCTATAAAGCTTCAATTTTGCCAGGAAGTTCTCCGTGCCTCTGTACTTTGTCT
CAGCAGCTGATGTTACCAACGTCCTGAAGCTCTAAAATGGTACAACTCAAATAGCTGTGTCTTACAAACAGAATTCCAGG
ACTTCATGGTCAAGGTTTTACAGAAGCCTGAGAAATTCAAGTTGGACAGGAAAGAGGAGAATGCGCCTGACCAGTATCAG
TGTGGCAGGATCCAGAGCCAAACCTCCTCC

Alignment

ORF - retro_itri_1230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.12 %
• Parental protein coverage: 64.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QERFQSMHASYYHKAHACIMVFDVQRKVTYKNLSTWYAELREFRPEIPCIV-VANKIDADINVTQKSFNF
          QE.FQ.MH..YYHKAHACI.VF..QR.VTYKNL..W..EL.EFRPEIPCIV....K.D.DI.VT..SFNF
Retrocopy QEQFQGMHTFYYHKAHACIIVFNMQREVTYKNLNFWETELEEFRPEIPCIV<MTSKTDIDIHVTL*SFNF

Parental  ARKFSLPLYFVSAADGTNVVKLFNDAIRLAVSYKQNS-QDFMDEVLQELENFKLEQKEEDAPDQDQSSRI
          ARKFS.PLYFVSAAD.TNV.KL.N.....AVSYKQNS.QDFM..VLQ..E.FKL..KEE.APDQ.Q..RI
Retrocopy ARKFSVPLYFVSAADVTNVLKL*NGTTQIAVSYKQNS<QDFMVKVLQKPEKFKLDRKEENAPDQYQCGRI

Parental  ENPSPS
          .....S
Retrocopy QSQTSS

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_1230 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1230 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000014686	1 retrocopy	retro_mluc_555,
Sus scrofa	ENSSSCG00000025041	1 retrocopy	retro_sscr_629,
Ictidomys tridecemlineatus	ENSSTOG00000002723	1 retrocopy	retro_itri_1230 ,