RetrogeneDB ID: retro_itri_457

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:59521..60465(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFG
• Ensembl ID: ENSSTOG00000025779
• Aliases: None
• Description: TRK-fused gene [Source:HGNC Symbol;Acc:11758]

Sequence

>retro_itri_457
AAAGATGAAGGTGGAGATCTTATAACAATTTTTGATAGTTCTGACCTTTCCTTTGCTATTCAGTGCAGTAAGATACTGAA
ACTGACATTGTTTGTTAATGGCCAACCAAGACTCCTTGAATCAAGTCAGGTGAAATTTCTCCATCAAGAACTGATAGAAC
TTAGGAATAAAGTGAATCACTTCTTGGATAGCTTGAAACCACCTGGAGAACCAGGACCTTCCACCAATATTCCTGAAAAT
GATACTGTGGATGGTAGGGAAGAAAAGCCTGCTGCTTCTGATTCTTTTGGAAAACAGTCTACTTAGGTTATGGCAGCAAG
TATGTCAGCTTTTGATCCTTTGAAAAAACAAGATGAAATCAATAAAAATGTAATGTCAGCGTTTGATTTAACAGATGATC
AGGTTTCAGGGCCACCCAGTGTTCCTTCAGACGACCTTTCAGGAAGGCCCGACAGCATTGCTTCCTCCTCTTCAGCAGCT
CACCCACCAGGAGTTCAGCTACAACAGCCTCCATATACAGGAGCCCAAACATAAGCAGGTCAGATTGAAGGTCAGATGTA
CCAACAGTACCAGCAGCAAGCCGGCTATGGTGCCCAACAGCCTCAAGCTCCACCTCAGCCACCTCAGAAGTATGGTATTC
AGTATTCAGCTAGCTATAGTCAGCAGACTAGACCCCACAACCTCAGCAGTTTCAGGGATATAGCCAGTAACCAACTTCCC
AGGCACCAGCTCCAATATTTTCTGGTCAGCCTCAGCAACTGGGTGCTCAACCACCACAGCAGTACCAGGTGAGCCATTAT
CCTACCCAAATGTCTCAGCCTACTAATTATACCATGGCCCCTGCCTCTCAGCCTGGAATGGCTCCAAACCAACCCAGGGC
TTATCAACCAAGACCAAGTTTTACTACACCTTCTGGAAGTACCATGGCCCCTCCTCCAAGTGGG

Alignment

ORF - retro_itri_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.43 %
• Parental protein coverage: 77.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDEDGDLITIFDSSDLSFAIQCSRILKLTLFVNGQPRPLESSQVKYLRRELIELRNKVNRLLDSLEPPGE
          KDE.GDLITIFDSSDLSFAIQCS.ILKLTLFVNGQPR.LESSQVK.L..ELIELRNKVN..LDSL.PPGE
Retrocopy KDEGGDLITIFDSSDLSFAIQCSKILKLTLFVNGQPRLLESSQVKFLHQELIELRNKVNHFLDSLKPPGE

Parental  PGPSTNIPENDTVDGREEKPAASDSSGKQSTQVMAASMSAFDPLKNQDEINKNVMSAFGLTDDQVSGPPS
          PGPSTNIPENDTVDGREEKPAASDS.GKQST.VMAASMSAFDPLK.QDEINKNVMSAF.LTDDQVSGPPS
Retrocopy PGPSTNIPENDTVDGREEKPAASDSFGKQST*VMAASMSAFDPLKKQDEINKNVMSAFDLTDDQVSGPPS

Parental  APAEDRSGTPDSIASSSSAAHPPGVQPQQPPYTGAQTQAGQIEGQMYQQYQQQAGYGAQQPQAPPQPPQQ
          .P..D.SG.PDSIASSSSAAHPPGVQ.QQPPYTGAQT.AGQIEGQMYQQYQQQAGYGAQQPQAPPQPPQ.
Retrocopy VPSDDLSGRPDSIASSSSAAHPPGVQLQQPPYTGAQT*AGQIEGQMYQQYQQQAGYGAQQPQAPPQPPQK

Parental  YGIQYSANYSQQTGPQ-QPQQFQGYGQQPTSQAPAPTFSGQPQQLAAQPPQQYQASSYPPQ--PYTTQTS
          YGIQYSA.YSQQT.P..QPQQFQGY.Q.PTSQAPAP.FSGQPQQL.AQPPQQYQ.S.YP.Q....T..T.
Retrocopy YGIQYSASYSQQTRPH<QPQQFQGYSQ*PTSQAPAPIFSGQPQQLGAQPPQQYQVSHYPTQMSQPTNYTM

Parental  QPTNYTVAPASQPGMAPSQPGAYQPRPS--FTPPSG
          .P.........QP......P....P..S....PPSG
Retrocopy APASQPGMAPNQPRAYQPRPSFTTPSGSTMAPPPSG

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_457 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_457 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457 ,