RetrogeneDB ID: retro_itri_516

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:3095460..3095952(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021736
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMACHC
• Ensembl ID: ENSSTOG00000006090
• Aliases: None
• Description: methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria [Source:HGNC Symbol;Acc:24525]

Sequence

>retro_itri_516
TTTGGCTTCGGGGTTTACCCCTTCCAGGTGGCATGGTACAATGAGCTTCTGCCTCCAGCCTTCCACCTGCCCCTGCCAGG
ACCTACCCTGGCCTTCTTGGTACACAGCACACCGACCAAGTTTGACCAGGCCCTTAAGCCCTTCTTGCAGAGCCGCCACC
TCCAACCACTAACTGACCCTGTGGATCAGTGTGTGGCCTACCACCTGAGACGTGTTAGACAGAGCCTCCCAGAGCTGCAG
ATGGAAATCATTGCTGACTACAAGGTATACCCCAACTGGCGCCCTAAGATTCTGGCCCAGACAGCAGCCCATGTGGCAGG
AGCTGCTTATTACTACCAATGCCAAGATGTGGAAGCTGACCCATGGGGAACTCAGCACATAGCAGGTGTGTGCATACACC
CCCGATTTGGGGGCTTGTTTGCCATCCGAGGTGTCGTGCTGCTGCCAGGGACAGACGCCAGATCTGCCACGGAGAAAGCC
CCCTGACTGTGT

Alignment

ORF - retro_itri_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 58.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGFEVYPFQVAWYNELLPPAFHLPLPGPTLAFLVLSTPAMFDQALKPFLQSHHLQSLTDPVDQCVAYHLR
          FGF.VYPFQVAWYNELLPPAFHLPLPGPTLAFLV.STP..FDQALKPFLQS.HLQ.LTDPVDQCVAYHLR
Retrocopy FGFGVYPFQVAWYNELLPPAFHLPLPGPTLAFLVHSTPTKFDQALKPFLQSRHLQPLTDPVDQCVAYHLR

Parental  RVRQSLPELQMEVIADYEVYPNRRPKILAQTAAHVAGAAYYYQRQDVEADPWGTQHIAGVCIHPRFGGWF
          RVRQSLPELQME.IADY.VYPN.RPKILAQTAAHVAGAAYYYQ.QDVEADPWGTQHIAGVCIHPRFGG.F
Retrocopy RVRQSLPELQMEIIADYKVYPNWRPKILAQTAAHVAGAAYYYQCQDVEADPWGTQHIAGVCIHPRFGGLF

Parental  AIRGVVLLPGTETPDLPRKKPPDC
          AIRGVVLLPGT.......K.P..C
Retrocopy AIRGVVLLPGTDARSATEKAP*LC

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_516 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_516 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000006090	1 retrocopy	retro_itri_516 ,