RetrogeneDB ID: retro_dord_275

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6837:280359..280869(-)
• Located in intron of: ENSDORG00000012906

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mpzl3
• Ensembl ID: ENSDORG00000003430
• Aliases: None
• Description: myelin protein zero-like 3 [Source:MGI Symbol;Acc:MGI:2442647]

Sequence

>retro_dord_275
TCTTGCAGGATTAGTGCAGCTTCTGACATATGAGGTTATGTTGGAGAAAATGTCAAGTTGAGATGTACCTTCAAGTCATC
TTCACATGTCACTGACAAACTGACCATAGAATGTAAGTTCTGTCCTCCTAGCAGCAGTCGCACAAAATCTGATTTTCACT
ATCAGTCTTTCCAGTACCCAACCACAGCAGGCACTTTTCGGGATCAGATCTCCTGGGCTGGAAATGTATACAAAGGGCAT
GCATCCATAAGCATAAGCAACCCTAACCATCAGGACAATAGGACATTCAGCTGTGCTGTGAAGAATCTCCCAGATGTGCA
CCATGACATCCCCCTGACGGAACTAACAATCACAGAAAGGGGTTTTGGTACCATGCTGTAATCTGCGGCCCTTCTTTCTA
TTCTTGTTTTCATTCCCTCAGCAGTAGTTATTGTTCTGCTGCTTGTGAGAATATCAAGGAAGGCTGCAGGGATGAAAAAG
CAGAGAAAGTCTAGCTATAAGAAAAATTCT

Alignment

ORF - retro_dord_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 74.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLEISADAHIRGYVGEKVKLRCTFKSSSDVTDKLTIDWTYRPPSSSRTESIFHYQSFQYPTTAGTFRDRI
          S..ISA...I.GYVGE.VKLRCTFKSSS.VTDKLTI.....PPSSSRT.S.FHYQSFQYPTTAGTFRD.I
Retrocopy SCRISAASDI*GYVGENVKLRCTFKSSSHVTDKLTIECKFCPPSSSRTKSDFHYQSFQYPTTAGTFRDQI

Parental  SWAGNVYKGDASISISNPTLKDNGTFSCAVKNPPDVHHNIPLTELTITERGFGTMLSSVALLSILVFIPS
          SWAGNVYKG.ASISISNP...DN.TFSCAVKN.PDVHH.IPLTELTITERGFGTML.S.ALLSILVFIPS
Retrocopy SWAGNVYKGHASISISNPNHQDNRTFSCAVKNLPDVHHDIPLTELTITERGFGTML*SAALLSILVFIPS

Parental  AVVIVLLLVRMSRKAAGMKKRSKSGYKKKS
          AVVIVLLLVR.SRKAAGMKK..KS.YKK.S
Retrocopy AVVIVLLLVRISRKAAGMKKQRKSSYKKNS

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_275 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000003430	2 retrocopies	retro_dord_271, retro_dord_275 ,
Dipodomys ordii	ENSDORG00000015874	1 retrocopy	retro_dord_591,