RetrogeneDB ID: retro_dord_773

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_8889:2..631(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fbxo28
• Ensembl ID: ENSDORG00000004351
• Aliases: None
• Description: F-box protein 28 [Source:MGI Symbol;Acc:MGI:1261890]

Sequence

>retro_dord_773
ATGCAAACTTCCAAGATGGGGGCGGCAGAGGAGCGGATCGCTGAGGAAGGAGGCGGCGGCCACGGCGATGCCGCCGGCTC
TGCTCAAAGACAGCCCCCAGTGCCCTCGTCCCAGGCCCCGCAGTCGGGGTCACAGGCACCTCCGGCGATGGCTCCGGACC
AGCTGCCACAAAACAACACGCTGGTGGCGCTGCCTATCATTGCCATCCAGAACATCCTCAGCTTTATGTCCTACGACGAA
ATTAGCCAGCTCCGCCTGGTTTGTAAAAGAATGGACTTGGTCTGTCAGAGAATGTTGAATCAGGGATTTTTGAAAGTGGA
GAGATACCATAATCTGTGTCAGAAACAAGTTAAAGCACAACTTCCAAGGAGAGAGTCAGAAAGGAGGAACCATTCTCTAG
CTCGTCATGCAGACATCCTTGCTGCTGTGGAAACCAGGTTGTCACTCTTAAATATGAGTTTTATGAAGTACGTGGATTCC
AATCTCTGTTGCTTCATCCCAGGAAAGGTGATTGATGAAATTTATCGTGTACTGAGATATGTCAATTCTACCAGAGCCCC
TCAACGAGCTCATGAAGATACCATTCAAGAGTTAAGGGATATTCCTCCATGGCAATGGAGTACTTCGAT

Alignment

ORF - retro_dord_773 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.21 %
• Parental protein coverage: 57.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAEERIAEEGGGGHGDGGSSSAAGSAQRQPPVPSSQAPQSGSQAPPAMAPDQQLPQNNTLVALPIVAI
          M.......AEE.....G.GG...AAGSAQRQPPVPSSQAPQSGSQAPPAMAPDQ.LPQNNTLVALPI.AI
Retrocopy MQTSKMGAAEERIAEEGGGGHGDAAGSAQRQPPVPSSQAPQSGSQAPPAMAPDQ-LPQNNTLVALPIIAI

Parental  ENILSFMSYDEISQLRLVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESERRNHSLARHADI
          .NILSFMSYDEISQLRLVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESERRNHSLARHADI
Retrocopy QNILSFMSYDEISQLRLVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESERRNHSLARHADI

Parental  LAAVETRLSLLNMTFMKYVDSNLCCFIP-KVIDEIYRVLRYVNSTRAPQRAHE-VLQELRDI-SSMAMEY
          LAAVETRLSLLNM.FMKYVDSNLCCFIP.KVIDEIYRVLRYVNSTRAPQRAHE...QELRDI.SSMAMEY
Retrocopy LAAVETRLSLLNMSFMKYVDSNLCCFIPGKVIDEIYRVLRYVNSTRAPQRAHEDTIQELRDI<SSMAMEY

Parental  FD
          FD
Retrocopy FD

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_773 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010255	5 retrocopies	retro_chof_1637, retro_chof_2403, retro_chof_247, retro_chof_730, retro_chof_903,
Dipodomys ordii	ENSDORG00000004351	1 retrocopy	retro_dord_773 ,
Tursiops truncatus	ENSTTRG00000013708	1 retrocopy	retro_ttru_1359,