RetrogeneDB ID: retro_itri_905

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393341.1:7197858..7198536(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM39A
• Ensembl ID: ENSSTOG00000003860
• Aliases: None
• Description: transmembrane protein 39A [Source:HGNC Symbol;Acc:25600]

Sequence

>retro_itri_905
TGCCCCCTATCTCCAGACCTCATTGGAAATGAGGTAGAATGTCTGAAAGCCGATTTCAACCACAGAATCAAAGAAGTTCT
CTTCAACTCCCTCTTCAGTGCCTACTATGTTGCATTTCTCCCTCTGTGTTTTGTAAAGAGTACCCAGTACTATGACATGC
ACTGGTCATGTGAACACCTCATTATGGTGTGGATCAATGCTTTTGTCATGCTTACCACACAGTTGCTGCCATCAAAATAC
TGTGATTTGCTACATAAATCAGCTTCTCACCTCGGCATATGGCAGAAGCTAGAACATGGGTCCTACAGCAATGCTCCACA
GCACATTTGGTCAGAAAATACAATATGGCCTCAAGGGGTGCTGGTGCAGCATAGCAGATGTTTATATAGAGCCATGGGGC
CTTACAACGTTGCAGTGCCTTCAGATGTATCCCATGCCCGCTTTTATTTCCTGTTTCATCGTCAATTAAGGCTGTTAAAT
CTACTAATCCTTATTGAGGGCAGTGTTGTCTTCTACCAGCCCTATTCCTTGCTGCGGTTGGAGAAGTGGAATCACACACT
TTCCATTGCTCTCATCCTCTTCTGCAACTACTATGTTTTATTTAAGCTCCTTCAGGACAGAATAGTATTAGGCAGGGCGT
ACTCCTACCCACTCAGCAGTTATGAACTTAAGGCAAAC

Alignment

ORF - retro_itri_905 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 50.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CPLSPDLIRNEVECLKADFNHRIKEVLFNSLFSAYYVAFLPLCFVKSTQYYDMRWSCEHLIMVWINAFVM
          CPLSPDLI.NEVECLKADFNHRIKEVLFNSLFSAYYVAFLPLCFVKSTQYYDM.WSCEHLIMVWINAFVM
Retrocopy CPLSPDLIGNEVECLKADFNHRIKEVLFNSLFSAYYVAFLPLCFVKSTQYYDMHWSCEHLIMVWINAFVM

Parental  LTTQLLPSKYCDLLHKSAAHLGKWQKLEHGSYSNAPQHIWSENTIWPQGVLVRHSRCLYRAMGPYNVAVP
          LTTQLLPSKYCDLLHKSA.HLG.WQKLEHGSYSNAPQHIWSENTIWPQGVLV.HSRCLYRAMGPYNVAVP
Retrocopy LTTQLLPSKYCDLLHKSASHLGIWQKLEHGSYSNAPQHIWSENTIWPQGVLVQHSRCLYRAMGPYNVAVP

Parental  SDVSHARFYANFLFHRPLRLLNLLILIEGSVVFYQLYSLLRSEKWNHTLSMALILFCNYYVLFKLLRDRI
          SDVSHARFY..FLFHR.LRLLNLLILIEGSVVFYQ.YSLLR.EKWNHTLS.ALILFCNYYVLFKLL.DRI
Retrocopy SDVSHARFY--FLFHRQLRLLNLLILIEGSVVFYQPYSLLRLEKWNHTLSIALILFCNYYVLFKLLQDRI

Parental  VLGRAYSYPLSSYELKAN
          VLGRAYSYPLSSYELKAN
Retrocopy VLGRAYSYPLSSYELKAN

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_905 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_905 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	ENSSTOG00000003860	1 retrocopy	retro_itri_905 ,