RetrogeneDB ID: retro_dord_87

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2592:52911..53505(-)
• Located in intron of: ENSDORG00000007558

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mettl8
• Ensembl ID: ENSDORG00000013075
• Aliases: None
• Description: methyltransferase like 8 [Source:MGI Symbol;Acc:MGI:2385142]

Sequence

>retro_dord_87
AGAAGAAAGTCTTAAGAAAGTTCAGCTGTGCAAGTCCTTCTAGAAAAGCAAGTTAAGTATGAAAGTGAAGCTAACAAATA
TTGGGACACATTTTACAAGATTCACAAGAATAAGTTTTTCAAGAATCGTAATTGGCTGTTGAGGGAATTTCCTGAAATTC
ATTCAGTTGATCAAAAGATGGAAGAGAACGTAGAAGAGTTCTCATGGGATCATGTCAAGACTAATGCTGCAGATTGTTTC
TCAAGAAAACAAGAACAAAAAAAAATCAAGAAAAATGGTTTATCAGATGGTCAAAGCCAACCGAGGTCTGATCTTTCCCA
TTGGAGCCTGAAGAAGCCAGGAAAGAGGTTCAGAAGACTGAAGTGTTTCCTGGTAGCAATACCACTTGCAGAATACTGGA
GGTTGGCTGTGGTGCTGGAAGCAGTGTTTTTCCAATTCTGAACACCTTGCAGAATCTTCCAAAATCCTTTCTCTATTGTT
GTGATTTTGCCTCTGGAGCTGTGGAGCTTGTCAAAGGCACACTTATCCTACAGGGCTGCCCAGCGTTCTACCTTTGTGCA
CGAGGTGTGTGATGATGGCTTGCCCTACCCTTTC

Alignment

ORF - retro_dord_87 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 53.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKKVEENSAVQVILEKQVKYESEASKYWDTFYKIHKNKFFKNRNWLLREFPEILPIDQKIEENVEELSWD
          R.K..E.SAVQV.LEKQVKYESEA.KYWDTFYKIHKNKFFKNRNWLLREFPEI...DQK.EENVEE.SWD
Retrocopy RRKS*ESSAVQVLLEKQVKYESEANKYWDTFYKIHKNKFFKNRNWLLREFPEIHSVDQKMEENVEEFSWD

Parental  HVKTNAADCFSGKQEQKKHLKKNGLSDGQSQLRSDFSN-LEAEEARKELQKTEVFPGSNATFRILEVGCG
          HVKTNAADCFS.KQE.....KKNGLSDGQSQ.RSD.S..LE.EEARKE.QKTEVFPGSN.T.RILEVGCG
Retrocopy HVKTNAADCFSRKQE-XXXXKKNGLSDGQSQPRSDLSH<LEPEEARKEVQKTEVFPGSNTTCRILEVGCG

Parental  AGSSVFPILNTLQNLPESFLYCCDFASRAVELV-KAHSSYRASQCSAFVHDICEDGLPYPF
          AGSSVFPILNTLQNLP.SFLYCCDFAS.AVELV.KAH.SYRA.Q.S.FVH..C.DGLPYPF
Retrocopy AGSSVFPILNTLQNLPKSFLYCCDFASGAVELV>KAHLSYRAAQRSTFVHEVCDDGLPYPF

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_87 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
Dipodomys ordii	ENSDORG00000013075	1 retrocopy	retro_dord_87 ,
Homo sapiens	ENSG00000123600	1 retrocopy	retro_hsap_1087,
Nomascus leucogenys	ENSNLEG00000005370	1 retrocopy	retro_nleu_1622,
Pongo abelii	ENSPPYG00000012927	1 retrocopy	retro_pabe_905,
Pan troglodytes	ENSPTRG00000012630	1 retrocopy	retro_ptro_739,