RetrogeneDB ID: retro_dord_679

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_52377:4125..4869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Utp23
• Ensembl ID: ENSDORG00000005950
• Aliases: None
• Description: UTP23, small subunit (SSU) processome component, homolog (yeast) [Source:MGI Symbol;Acc:MGI:1925831]

Sequence

>retro_dord_679
GTGAAGATCACCAGGCAGAAACACACCAAGAAGCATCTTGGCTTCTTTCGCAACTATTGTGGAGTCCACGAGCTGTACCA
GATTCTGCTGGATGGCACTTTCTGTCAGGCGGCGCTGAGGGGCCGTGTCCAGCTGTGGGAGCAGCTGCCCCGCTACCTTA
TGGGGTAGATGCAGCTGTGTACCACCAGATGTGTGTTGAAGGAGTTAGAAGCATTGGGAAAGGACTTATACGGGGCAAAA
CTCAATGCACAGAAATGCCAGGTTCGAAATTGTCCCCATTTCAAGAACTCAGTGACTGGATCAGAATGTCTGCTTTCCAT
GGTGGAGGAAGGGAATCCTCACCCTTATTTTGTAGCAACCCAGGATCAGAATTTATCTGTGAAGGTAAAGAAGCAGCCTG
GAGTGCCTCTCATGTTTATTATTCAGAATACTATAGTCTTGGACAAACCTTCTCCCAAAACAATTGCTTTTGTAAAATCT
GTCCAGTCAGGTCAGCTTGTCTCGGTGCATGATAAACAAAATATTAAGCTGTTCAAAGAGGAGCAAGGTTTAGTGAAAAA
TCCTGAACAGAGAAGAAAAAAGCACAGGAAAATAAGTGGCCCCAATCCTCTTAGCTGTTTGAAGAAAAAGAAAAAGGTCG
TGGATTCAAAATCACCTGCTTCTGACAAGAAAAGGAAAAGGAAAATGATGGGCAACAGATCTACCTTAAAAGTACTTTCT
GAGAAGCAGAATGCAGAAGGACAA

Alignment

ORF - retro_dord_679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKITRQKHAKKHLGFFRNNFGVREPYQILLDGTFCQAALRGRIQLREQLPRYLTGETQLCTTRCVLKELE
          .KITRQKH.KKHLGFFRN..GV.E.YQILLDGTFCQAALRGR.QL.EQLPRYL.G..QLCTTRCVLKELE
Retrocopy VKITRQKHTKKHLGFFRNYCGVHELYQILLDGTFCQAALRGRVQLWEQLPRYLMG*MQLCTTRCVLKELE

Parental  TLGKDLYGAKLIAQKCQVRNCPHFKNSVTGSDCLLSMVEEGNPHHYFVATQDQNLSVKVKKQPGVPLMFI
          .LGKDLYGAKL.AQKCQVRNCPHFKNSVTGS.CLLSMVEEGNPH.YFVATQDQNLSVKVKKQPGVPLMFI
Retrocopy ALGKDLYGAKLNAQKCQVRNCPHFKNSVTGSECLLSMVEEGNPHPYFVATQDQNLSVKVKKQPGVPLMFI

Parental  IQNTIVLDKPSPKTIAFVKSVQSGQLVSVHDKQNIKQLKEEQGLVKNPEQRRRKKRKKISGPNPLSCLKK
          IQNTIVLDKPSPKTIAFVKSVQSGQLVSVHDKQNIK..KEEQGLVKNPEQ.RRKK..KISGPNPLSCLKK
Retrocopy IQNTIVLDKPSPKTIAFVKSVQSGQLVSVHDKQNIKLFKEEQGLVKNPEQ-RRKKHRKISGPNPLSCLKK

Parental  KKKVQDSKSPASDKKRKRKRIRNRSTSKVLSEKQNAEGQ
          KKKV.DSKSPASDKKRKRK...NRST.KVLSEKQNAEGQ
Retrocopy KKKVVDSKSPASDKKRKRKMMGNRSTLKVLSEKQNAEGQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_679 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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
Dipodomys ordii	ENSDORG00000005950	1 retrocopy	retro_dord_679 ,