RetrogeneDB ID: retro_itri_893

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393339.1:129837..130263(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF3
• Ensembl ID: ENSSTOG00000007121
• Aliases: None
• Description: activating transcription factor 3 [Source:HGNC Symbol;Acc:785]

Sequence

>retro_itri_893
ACACCCTTTGTCAAGGAAGAGTTGAGGTTTGCCATCCAGAACAAGCACCTCTGCCATTGGATGTCCTCTGCGCTGGAGTC
AGTCATGATCAGCGACAGACCACTGGAGATGTCAGTCACAAAAGCTGAGGTAGCTCCTGAGGATGATGAAAGGAAAAAGA
GGCAGTGGGAAAGAAATAAGATCACAGCCACCAAGTGCCAAAACAAGCAAAAGGAAAAGATGGAGTGCCTGCAGTCAGAG
AAGCTGGAAAGTCTGAATGCCGAACTAAAGACCCAAATTGAGGAGCTGAAGAATGAGAAGTAGTATTTGATATACATGCT
CAACCTGTGTCAGTCCACGGGTATTGTCTGGGCTCAGAATGGGCAGACTCCAGAAGATGAGAGAAACCTCTTTATCCGAC
AGATAAAAGAAGGAACACTAAACAGC

Alignment

ORF - retro_itri_893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 79.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TPFVKEELRFAIQNKHLCHRMSSALESVTVSDRPLEMSVTKAEVAPEEDERKKRRRERNKIAAAKCRNKK
          TPFVKEELRFAIQNKHLCH.MSSALESV..SDRPLEMSVTKAEVAPE.DERKKR..ERNKI.A.KC.NK.
Retrocopy TPFVKEELRFAIQNKHLCHWMSSALESVMISDRPLEMSVTKAEVAPEDDERKKRQWERNKITATKCQNKQ

Parental  KEKTECLQKESEKLESVNAELKAQIEELKNEKQHLIYMLNLHRPTCIVRAQNGRTPEDERNLFIQQIKEG
          KEK.ECLQ..SEKLES.NAELK.QIEELKNEK..LIYMLNL...T.IV.AQNG.TPEDERNLFI.QIKEG
Retrocopy KEKMECLQ--SEKLESLNAELKTQIEELKNEK*YLIYMLNLCQSTGIVWAQNGQTPEDERNLFIRQIKEG

Parental  TLQS
          TL.S
Retrocopy TLNS

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_893 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_893 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	ENSSTOG00000007121	1 retrocopy	retro_itri_893 ,