RetrogeneDB ID: retro_itri_134

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393642.1:647058..647433(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025608
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TAX1BP3
• Ensembl ID: ENSSTOG00000022920
• Aliases: None
• Description: Tax1 (human T-cell leukemia virus type I) binding protein 3 [Source:HGNC Symbol;Acc:30684]

Sequence

>retro_itri_134
ATGTCTTACATACTGGGCCAGCTGGTCACTGCCATTATGCAAAGAGTTGAAATTCACAAGATGCATCAAAGAAAGAACTT
AATCTTGGGCTTCAGCATTGGTGGTGGAATTGACCAGGTTCCCTCTCAACATCCCTTCTCAGAAGATAAGACAGACAAGA
GCATTTATGTCACACACGTGAATGTAGGAGGTCCTGCTGAAATTGCTGGGCTGCAGATCGGAGACAAGATCATGCAGGGG
AATGGCTGGGACATGACCATGGTCACACATGACCAGGCCAGGAAATGGCTCACAAAGCACTCGGAGGAAGTGGTGCGCCT
GCTGGTGAGGCAGCGGTTGCTGCAGAAGGCCCTGCAGCAGTCCATGCTGTCTTAG

Alignment

ORF - retro_itri_134 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYIPGQPVTAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAG
          MSYI.GQ.VTA..QRVEIHK..Q..NLILGFSIGGGIDQ.PSQ.PFSEDKTDK.IYVT.V..GGPAEIAG
Retrocopy MSYILGQLVTAIMQRVEIHKMHQRKNLILGFSIGGGIDQVPSQHPFSEDKTDKSIYVTHVNVGGPAEIAG

Parental  LQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSMLS
          LQIGDKIMQ.NGWDMTMVTHDQARK.LTK.SEEVVRLLV....LQKA.QQSMLS
Retrocopy LQIGDKIMQGNGWDMTMVTHDQARKWLTKHSEEVVRLLVRQRLLQKALQQSMLS

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_134 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_134 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000023829	1 retrocopy	retro_dnov_2238,
Dipodomys ordii	ENSDORG00000013801	2 retrocopies	retro_dord_56, retro_dord_728,
Myotis lucifugus	ENSMLUG00000026421	1 retrocopy	retro_mluc_221,
Mus musculus	ENSMUSG00000040158	1 retrocopy	retro_mmus_1929,
Oryctolagus cuniculus	ENSOCUG00000023903	1 retrocopy	retro_ocun_781,
Sus scrofa	ENSSSCG00000017866	1 retrocopy	retro_sscr_365,
Ictidomys tridecemlineatus	ENSSTOG00000022920	1 retrocopy	retro_itri_134 ,