RetrogeneDB ID: retro_dord_322

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_1161:97018..97256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdc42se1
• Ensembl ID: ENSDORG00000007370
• Aliases: None
• Description: CDC42 small effector 1 [Source:MGI Symbol;Acc:MGI:1889510]

Sequence

>retro_dord_322
ATGAGTGAATTTTGGCATAAGTTGGGCTGTTGTGTGGTAGAGGAACCCCAGCTGAACAAGAAGAGAAGACAGATTGACTG
GACCATGATTGGGGAACCAATGAATTTTGTCCACCCGACTCACATTGGCTCTGGGGAGATGGGGGCTGGAGATGGACCTA
CCATGACAGGTTGCAGTTCAGGAGCAGATGAAATCCAAAGGAAATCGACACAGGCCATGGAGCAATTCTAGGGGCTTG

Alignment

ORF - retro_dord_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEFWHKLGCCVVEKPQPKKKRRRIDRTMIGEPMNFVHLTHIGSGEMGAGDGLAMTG-AVQEQMRSKGNR
          MSEFWHKLGCCVVE.PQ..KKRR.ID.TMIGEPMNFVH.THIGSGEMGAGDG..MTG.AVQEQM.SKGNR
Retrocopy MSEFWHKLGCCVVEEPQLNKKRRQIDWTMIGEPMNFVHPTHIGSGEMGAGDGPTMTG>AVQEQMKSKGNR

Parental  DRPWSNSRGL
          .RPWSNSRGL
Retrocopy HRPWSNSRGL

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_322 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015363	1 retrocopy	retro_btau_894,
Dipodomys ordii	ENSDORG00000007370	1 retrocopy	retro_dord_322 ,
Echinops telfairi	ENSETEG00000019984	1 retrocopy	retro_etel_1111,
Mus musculus	ENSMUSG00000046722	1 retrocopy	retro_mmus_3360,
Tursiops truncatus	ENSTTRG00000007000	1 retrocopy	retro_ttru_549,