RetrogeneDB ID: retro_itri_797

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393324.1:7762048..7762459(-)
• Located in intron of: ENSSTOG00000009251

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSCB
• Ensembl ID: ENSSTOG00000011587
• Aliases: None
• Description: HscB iron-sulfur cluster co-chaperone homolog (E. coli) [Source:HGNC Symbol;Acc:28913]

Sequence

>retro_itri_797
TTGTGGGGTGGGAGGGCCCAGGTGATGTTTCAGCTATGGGGGTTGCAGCCCTCAGGGGTCCCCAGAAGGAGTGTGTTAAG
CTGCCATGCTGCATCGGAAGAGGGAAGCGGTTAGGCGAGGTGTTGGAATTGCGGCAGCCTCCGGCGGGGAAACGTGTTCT
TCTGCCACCAGTGCCGAGCTCTGCAGCCACCAGACCGGACTCACTACTTCAGCCTCATGGATTGCAACCGTTCCTTCAGA
GTTAATACTACAAAACTCCAGCACAGGTTTCAGCAACTACAGCGTCTTGTCCACCCAGGTTTCTTCAGCCAGAGATCTCA
GACTGAAAAGGACTTCTCAGAGAAGCATTCAACCCTGGTGAATGATGCTTATAAGACCCTGCTGGCCCTGAGCAGGGGAC
TATACCTTGTA

Alignment

ORF - retro_itri_797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.89 %
• Parental protein coverage: 59.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWGGRAQVLCRLWGLRPAGVPGRRVLSCHAASEEGSGSARCWNCGSPGRGEGFFCHQCRALQPPDPTRDY
          .WGGRAQV...LWGL.P.GVP.R.VLSCHAASEEGSG.ARCWNCGS..RG..FFCHQCRALQPPD.T..Y
Retrocopy LWGGRAQVMFQLWGLQPSGVPRRSVLSCHAASEEGSG*ARCWNCGSLRRGNVFFCHQCRALQPPDRTH-Y

Parental  FSLMDCNRSFRVNTTKLQHRFQQLQRLVHPDFFNQRSQTEKDFSEKHSTLVNEAYKTLLAPLSRGLYLL
          FSLMDCNRSFRVNTTKLQHRFQQLQRLVHP.FF.QRSQTEKDFSEKHSTLVN.AYKTLLA.LSRGLYL.
Retrocopy FSLMDCNRSFRVNTTKLQHRFQQLQRLVHPGFFSQRSQTEKDFSEKHSTLVNDAYKTLLA-LSRGLYLV

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_797 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_797 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011178	2 retrocopies	retro_dnov_2445, retro_dnov_851,
Ictidomys tridecemlineatus	ENSSTOG00000011587	1 retrocopy	retro_itri_797 ,