RetrogeneDB ID: retro_itri_620

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393306.1:7324650..7325207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDEL1
• Ensembl ID: ENSSTOG00000027930
• Aliases: None
• Description: nudE nuclear distribution E homolog (A. nidulans)-like 1 [Source:HGNC Symbol;Acc:17620]

Sequence

>retro_itri_620
GAGCAAAGAGGGCGACAATAGTTAGTTTCACTGGAAGACTTTGAACAAAGGCTAACTCAGGCCATTGAATGAAATGCATT
TTTAGAAAATGAACTCGATGAAAAGGAATCCTTGTTGGTTTCTGTACAGAGGTTAAAGGATGAAGCAAGAGACTTAAGGC
AAGAACTAGCAGTTCGGGAGAGACAACAGGAAGTGACCCGAAAGTCAGCTCCCAGTTCTCCCACGTTGGACTGTGAGAAG
ATGGATTCTGCTGTCCAGGCTTCACTCTCTTTGCCAGCTACTCCTGTTGGCAAAGGAACAGAAAATAGTTTTCCTTCACC
AAAAGCTATACCAAATGGTTTTGGAACCAGTCCACTAACTCCTTCTGCTAGGATATCAGCACTAAACATCGTGGGGATCT
CTTAAGGAAAGTAGGAGCTTTAGAATCCAAATTAGCAGCTTGCAGGAATTTTGCAAAGGACCAAGCATCACGAAAATCCT
ATATTTCAGGGAATGTGAACTGTGGAGTGATGAATAGCAATGGCACAAAGTTCCCTCCATCAGGGCACACGTCTTTC

Alignment

ORF - retro_itri_620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.05 %
• Parental protein coverage: 59.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERAKRATIVSLEDFEQRLNQAIERNAFLESELDEKESLLVSVQRLKDEARDLRQELAVRERQQEVTRKSA
          E...R...VSLEDFEQRL.QAIE.NAFLE.ELDEKESLLVSVQRLKDEARDLRQELAVRERQQEVTRKSA
Retrocopy EQRGRQ*LVSLEDFEQRLTQAIE*NAFLENELDEKESLLVSVQRLKDEARDLRQELAVRERQQEVTRKSA

Parental  PSSPTLDCEKMDSAVQASLSLPATPVGKGTENSFPSPKAIPNGFGTSPLTPSARISALNIVG-DLLRKVG
          PSSPTLDCEKMDSAVQASLSLPATPVGKGTENSFPSPKAIPNGFGTSPLTPSARISALNIVG.DLLRKVG
Retrocopy PSSPTLDCEKMDSAVQASLSLPATPVGKGTENSFPSPKAIPNGFGTSPLTPSARISALNIVG<DLLRKVG

Parental  ALESKLAACRNFAKDQASRKSYISGNVNCGVMNSSGTKFSRSGHTSF
          ALESKLAACRNFAKDQASRKSYISGNVNCGVMNS.GTKF..SGHTSF
Retrocopy ALESKLAACRNFAKDQASRKSYISGNVNCGVMNSNGTKFPPSGHTSF

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_620 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_620 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014341	1 retrocopy	retro_cjac_4072,
Cavia porcellus	ENSCPOG00000012878	1 retrocopy	retro_cpor_626,
Pan troglodytes	ENSPTRG00000008744	1 retrocopy	retro_ptro_2000,
Ictidomys tridecemlineatus	ENSSTOG00000019896	1 retrocopy	retro_itri_1101,
Ictidomys tridecemlineatus	ENSSTOG00000027930	1 retrocopy	retro_itri_620 ,
Tursiops truncatus	ENSTTRG00000006517	1 retrocopy	retro_ttru_1239,