RetrogeneDB ID: retro_dord_539

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_28580:7334..7734(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ict1
• Ensembl ID: ENSDORG00000006439
• Aliases: None
• Description: immature colon carcinoma transcript 1 [Source:MGI Symbol;Acc:MGI:1915822]

Sequence

>retro_dord_539
CTAGACGGCCTGACTGTATCTTACCGTCGGAGCCGCGGGCCTGGGCGTCAGAACGCTTAACAAAGTGAATTCCAAGGCGG
AGGTCAGGTTCCACTTGGCATCTGCCCACTGGATGGCAGAGCCGCGCGGCAGAAGATCACTGTCAGGCATAAAGATAAGA
TCAGCCGAGCAGGAGAGGTGATTCTCACCTCTGAAAGCAGCCGCTTTCAGTTCCGCAATCTAGCCGACTGCCTACAGAAA
ATTCGAGATATGATTGCTGAGGCCAGCCAGACACCCAAGGATCCCTCTAGAGAAGATGCTCGAATCCAGAGAATTAGGAT
AGAAAACATGAATAGGGAAAAGCTGGGACAAAATCAGAATCAGTTCTGCCATAAAGACCAGCAGGAGGGTAGATGTGGAT

Alignment

ORF - retro_dord_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 64.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDRLTISYCRSSGPGGQN-VNKVNSKAEVRFHLASADWMAEP-VRQKIAVRHKNKINRAGELIVTSESSR
          LD.LT.SY.RS.GPG.QN..NKVNSKAEVRFHLASA.WMAEP..RQKI.VRHK.KI.RAGE.I.TSESSR
Retrocopy LDGLTVSYRRSRGPGRQN>LNKVNSKAEVRFHLASAHWMAEP<ARQKITVRHKDKISRAGEVILTSESSR

Parental  FQFRNLADCLQKIRDMIAEASQTPKEPSREDAQIQRIRIENMNRERLRQK-RISSAIKTSRRVDVD
          FQFRNLADCLQKIRDMIAEASQTPK.PSREDA.IQRIRIENMNRE.L.Q..RISSAIKTSRRVDVD
Retrocopy FQFRNLADCLQKIRDMIAEASQTPKDPSREDARIQRIRIENMNREKLGQN>RISSAIKTSRRVDVD

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_539 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006439	1 retrocopy	retro_dord_539 ,
Macaca mulatta	ENSMMUG00000011644	1 retrocopy	retro_mmul_181,
Monodelphis domestica	ENSMODG00000007126	1 retrocopy	retro_mdom_1152,