RetrogeneDB ID: retro_itri_1811

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393860.1:107179..107745(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPCPD1
• Ensembl ID: ENSSTOG00000006827
• Aliases: None
• Description: glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26957]

Sequence

>retro_itri_1811
ATGAAATCTTCATTTTCCAAGTATTGGAAGCCAAGAATACCATGGGATGTTGGACACAGAGATTCAGGGAATTCAAAAAC
AACTTCCCAGCTGGCTACAGTTCAAGAAAATACTATTGCTTCTTTAAGAAACACTGCTAGTCATGGTGCAGCCTTTGTAG
AATTTGATGTTCATCTTTCAAAAGACATTGTGCCTGTGGTAAATCGTGATCCATCTGATGTTTGACCATGAAGAAGAAGT
TTGATGCTGATCTAGTTGAATTATTTGAAATTCCAGTAAAGGAACTAACATTTGACCAACTCCAGTTGTTAAAACTCACC
CATGTGATTGCATTAAAATCTAAAGATCAACAAGAATCTGTGATTGAGGAAAAAAATTCCTTTTCTGAAAATCAGCCATT
TCCTTCTCTTAAGATGGTTTTAGAATCTTTCCCAGAAGATGTAGAGTTTAACATAGAAATAAAATGGATCTGCCAACAAA
GGGATGGAATGTGGGATACTAATTTATCAACATATTTTGACATGAATATGTTTTTGGATATAATTTAAAAAACTGTTTTA
GAAAAC

Alignment

ORF - retro_itri_1811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.89 %
• Parental protein coverage: 51.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKSSFSKYWKPRIPLDVGHRGAGNSTTTAQLAKVQENTIASLRNAASHGAAFVEFDVHLSKDFVPVVYHD
          MKSSFSKYWKPRIP.DVGHR..GNS.TT.QLA.VQENTIASLRN.ASHGAAFVEFDVHLSKD.VPVV..D
Retrocopy MKSSFSKYWKPRIPWDVGHRDSGNSKTTSQLATVQENTIASLRNTASHGAAFVEFDVHLSKDIVPVVNRD

Parental  LTC-CLTMKKKFDADPVELFEIPVKELTFDQLQLLKLAHVTALKSKDRQESVIEEENSFSENQPFPSLKM
          ....CLTMKKKFDAD.VELFEIPVKELTFDQLQLLKL.HV.ALKSKD.QESVIEE.NSFSENQPFPSLKM
Retrocopy PSD<CLTMKKKFDADLVELFEIPVKELTFDQLQLLKLTHVIALKSKDQQESVIEEKNSFSENQPFPSLKM

Parental  VLESLPEDVGFNIEIKWICQQRDGMWDGNLSTYFDMNMFLDIILKTVLEN
          VLES.PEDV.FNIEIKWICQQRDGMWD.NLSTYFDMNMFLDII.KTVLEN
Retrocopy VLESFPEDVEFNIEIKWICQQRDGMWDTNLSTYFDMNMFLDII*KTVLEN

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_1811 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1811 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125772	1 retrocopy	retro_hsap_3854,
Pongo abelii	ENSPPYG00000010687	1 retrocopy	retro_pabe_3052,
Pan troglodytes	ENSPTRG00000013228	1 retrocopy	retro_ptro_2625,
Ictidomys tridecemlineatus	ENSSTOG00000006827	1 retrocopy	retro_itri_1811 ,