RetrogeneDB ID: retro_itri_1711

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393651.1:28756..29562(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027780
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHUK
• Ensembl ID: ENSSTOG00000016412
• Aliases: None
• Description: conserved helix-loop-helix ubiquitous kinase [Source:HGNC Symbol;Acc:1974]

Sequence

>retro_itri_1711
GAAGCAGGGCACTATGTGTCTGGGATAAAAGAAGACTACAGCAGGCTCTTTCAGGGACAGAGGGCAGCAATGTTAAGTCT
TCTTAGATATAATGCTAACTTGACAAAAATGAAGAACACATTGATCTCAGCATCACAACAACTGAAAGCTAAATTGGAGT
TTTTTTCACAAAAGCATTCAGCTAGACTTAGAGAGAGATTGTGAACAGATGACTTATGGGATATCTTCAGAAAAAAATGC
TAAAAGCATGGAAAGAAATGGAAGAAAAGACCATTCACTGTGCGAGACTGGTGTCATTGGATACCTTAAGGGTCAGATTA
TGTCTTTTTACACTGAAATCATGGAGCTATAGAAAAGTCTATGTGGAATACATCTGGGAGATTTTGATGGAATCTCCGGA
ACAACTTGCAATTGATCTATATAAGCAGTTACAGCACAGACCTGCAGATCACTCCTTTCAGCAATAGCACAGAGATGGTG
ACGATCATTATGCATACTGTGCAGAGTCTGGGCCATGTTCTCAAGGAGCTATTTGGTCATCTGAGCAAGTTGTTGGGTGT
AAGCAGAAGATTATTAATCTACTCCCCAAAATGGAAGTGGCCTTCAGTAACATCAAAGAAGCTGACAATACTATCATGTT
TATGCAGAGAAAAAGGCAGAAAGAAATATGGCATCTTCTTAAAATTACCTGCACACAGAGTTCTGCCTGGTTCCTTATTG
GATCCAGTCTAGAAGGTACAGTAAACCCTCAAGCATCAGCATGGCTGCCGACATTAGAAAAACGCGTACAACCTCTGACA
TGTGTG

Alignment

ORF - retro_itri_1711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.48 %
• Parental protein coverage: 60.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EAVHYVSGLKEDYSRLFQGQRAAMLSLLRYNANLTKMKNTLISASQQLKAKLEFF-HKSIQLDLERYSEQ
          EA.HYVSG.KEDYSRLFQGQRAAMLSLLRYNANLTKMKNTLISASQQLKAKLEFF.HKSIQLDLER..EQ
Retrocopy EAGHYVSGIKEDYSRLFQGQRAAMLSLLRYNANLTKMKNTLISASQQLKAKLEFF>HKSIQLDLERDCEQ

Parental  MTYGISSEK-MLKAWKEMEEKAIHYA-EVGVIGYLEDQIMSLHTEIMELQKSPYGRRQGD-LMESLEQHA
          MTYGISSEK.MLKAWKEMEEK.IH.A.E.GVIGYL..QIMS..TEIMEL.KS..G...GD.LMES.EQ.A
Retrocopy MTYGISSEK>MLKAWKEMEEKTIHCA<ETGVIGYLKGQIMSFYTEIMEL*KSLCGIHLGD>LMESPEQLA

Parental  IDLYKQLKHRPADHSY-SDSTEMVKIIVHTVQSQDRVLKELFGHLSKLLG-CKQKIIDLLPKVEVALSNI
          IDLYKQL.HRPADHS..S.STEMV.II.HTVQS...VLKELFGHLSKLLG.CKQKII.LLPK.EVA.SNI
Retrocopy IDLYKQLQHRPADHSF>SNSTEMVTIIMHTVQSLGHVLKELFGHLSKLLG<CKQKIINLLPKMEVAFSNI

Parental  KEADNTVMFMQGKRQKEIWHLLKIACTQSSARSLVGSSLEGAVNPQSSAWLPTLAEREQPLSCV
          KEADNT.MFMQ.KRQKEIWHLLKI.CTQSSA..L.GSSLEG.VNPQ.SAWLPTL..R.QPL.CV
Retrocopy KEADNTIMFMQRKRQKEIWHLLKITCTQSSAWFLIGSSLEGTVNPQASAWLPTLEKRVQPLTCV

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_1711 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1711 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000025199	1 retrocopy	retro_mmus_1521,
Sarcophilus harrisii	ENSSHAG00000000038	1 retrocopy	retro_shar_644,
Ictidomys tridecemlineatus	ENSSTOG00000016412	1 retrocopy	retro_itri_1711 ,