RetrogeneDB ID: retro_itri_386

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393288.1:18749110..18749635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARP11
• Ensembl ID: ENSSTOG00000024474
• Aliases: None
• Description: poly (ADP-ribose) polymerase family, member 11 [Source:HGNC Symbol;Acc:1186]

Sequence

>retro_itri_386
ATGTTTCACAAAGCAGACAAAGTCTTACCCAACATGACAAATAGTGAAATGCTTGCCATGGGCACATCAGAAACCCAATA
GGACTGGTTTTACCTGGAAGAATGTGGGAAGTAGCATATGTTTCGGCCAGATACCAACATTCCATGTTCAGTTGGTAGTA
AAGACATCAAAAAGAGCTTCAGAACAAATCCTTGTGGCTCCATTTTTTTTACTATTTCCAAAGTCAGCTACAAGATAGAC
TTTGCTGAAAGGAAGTAAATGAAACTCACCATTGGAAAACAGTGCTTAATAACAAGGGCTCCTTTTTCTATCAGTACTTG
CAGTTATATCTGTGAAAATAAGGCTATCCCTATGCCACCCGACTGGCAGAATGTGAATACTAAAGCACCAAATCAACTTA
TTTCTCTGCACACTCAAACACATGAATATAACGAAGTTGTCAGTCTCTTTGAGAAAACAATGAATTGTAAATGAATTAGA
ATTCAGAGAATCCAAAATTTAGACCTATGGGAGTTCTTTTGCAGG

Alignment

ORF - retro_itri_386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.3 %
• Parental protein coverage: 53.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFHKAEEFLSKTTDSEMDDMDTSDTQWGWFYLAECGKWHMFQPDTNIQCSVSSEDIEKSFRTNPCGSISF
          MFHKA...L...T.SEM..M.TS.TQ..WFYL.ECGK.HMF.PDTNI.CSV.S.DI.KSFRTNPCGS...
Retrocopy MFHKADKVLPNMTNSEMLAMGTSETQ*DWFYLEECGK*HMFRPDTNIPCSVGSKDIKKSFRTNPCGSXXX

Parental  TTSKFSYKIDFAEMKQMNLTTGKQRLIKRAPFSISAFSYICENEAIPMPPHWENVNTEVPYQLISLHNQT
          T.SK.SYKIDFAE.K.M.LT.GKQ.LI.RAPFSIS..SYICEN.AIPMPP.W.NVNT..P.QLISLH.QT
Retrocopy TISKVSYKIDFAERK*MKLTIGKQCLITRAPFSISTCSYICENKAIPMPPDWQNVNTKAPNQLISLHTQT

Parental  HEYNEVASLFGKTMDRNRIKRIQRIQNLDLWEFFCR
          HEYNEV.SLF.KTM....I.RIQRIQNLDLWEFFCR
Retrocopy HEYNEVVSLFEKTMNCK*I-RIQRIQNLDLWEFFCR

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_386 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_386 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	ENSSTOG00000024474	1 retrocopy	retro_itri_386 ,