RetrogeneDB ID: retro_itri_1139

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393384.1:5397579..5398159(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAP2C
• Ensembl ID: ENSSTOG00000019777
• Aliases: None
• Description: phosphatidic acid phosphatase type 2C [Source:HGNC Symbol;Acc:9230]

Sequence

>retro_itri_1139
TACTCCCATTCCCTCTACAAGGTGCTAGACACCTTCCTGTTTGGGGCAGCCATGAGCCAGTCCTTGAGGGACCTGGCCAA
GTACATGATCAGTTGTCTGCACCCCAACTTCCTGACCCTCTGCAACCCAGACTGGAGCTGGATCAACTGTTCAGTCTACG
GTGCAGTTGGAGAGAGTGTGCAGGGGGAGCCCTGCCAATGTCATCGAGGCCAGACTCTCCTCCTACTGTGGACACTCCTC
CCCTGGGATGTAGTGCGTGCTATTTTTGGCTGTTCTTGCAGACACAGCTCTGCAGGAAGTTGGCACAGCTGCTACGGCCC
ACTGTGAAGTTCTTCCTGGTGGCCTTCGCCCTGTAAGTAGGCTACACCCACAGGTCGGACCACAAGCACCACTGCTGTCA
TGTCCTCGTCTGTCTCCTGCCAAGGTCACTGGAAGCTAGCCTCACTTTTCAGTATGTCTCAGACTTCTTCAAAGACAGAC
CCCCTCATCCCTGCCTGGAGGAGGTGGCAGAGCGCAAGCCCAGCCTGTGATTGAAGTTGACTGTGGGCGAGGCTGCACAC
AACCACGTGGCCATCCAATC

Alignment

ORF - retro_itri_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.71 %
• Parental protein coverage: 67.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YVAALYKVLGTFLFGAAVSQSLTDLAKYMIGRLRPNFLAVCDPDWSRVNCSVY-VQLERVCRGSPANVTE
          Y...LYKVL.TFLFGAA.SQSL.DLAKYMI..L.PNFL..C.PDWS..NCSVY.VQLERVCRGSPANV.E
Retrocopy YSHSLYKVLDTFLFGAAMSQSLRDLAKYMISCLHPNFLTLCNPDWSWINCSVY>VQLERVCRGSPANVIE

Parental  ARLSFYSGHSSFGMYCMLFLALYVQARL-CGKW-ARLLRPTVQFFLVAFALYVGYTRVSDHKHHWSDVLV
          ARLS.Y.GHSS.GM.C.LFLA......L..G.W.A.LLRPTV.FFLVAFAL.VGYT..SDHKHH...VLV
Retrocopy ARLSSYCGHSSPGM*CVLFLAVLADTAL<AGSW<AQLLRPTVKFFLVAFAL*VGYTHRSDHKHHCCHVLV

Parental  GLLQGALVAGLTVRYVSDFFKARPLRPCLEEAVERKPSLSLTLTVGEASHNH-RGYPV
          .LL...L.A.LT..YVSDFFK.RP..PCLEE..ERKPSL.L.LTVGEA.HNH.RG.P.
Retrocopy CLLPRSLEASLTFQYVSDFFKDRPPHPCLEEVAERKPSL*LKLTVGEAAHNH<RGHPI

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_1139 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1139 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019734	1 retrocopy	retro_cfam_397,
Felis catus	ENSFCAG00000024319	1 retrocopy	retro_fcat_483,
Ictidomys tridecemlineatus	ENSSTOG00000019777	2 retrocopies	retro_itri_1139 , retro_itri_1721,