RetrogeneDB ID: retro_dord_441

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_18918:15823..16765(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dctn2
• Ensembl ID: ENSDORG00000007137
• Aliases: None
• Description: dynactin 2 [Source:MGI Symbol;Acc:MGI:107733]

Sequence

>retro_dord_441
ATGGCGGACCCTAAATATGCCGGCCTTCCCGTCATTGTCAGGAACGAACCAGATGTTTATGAAACCAGCTACCTACCTGA
GGATGATCAAGCAGAGTTTGATGCGGAGGAGCTGTCAAGCACAAGTGTGGAGCACATTATTGTCAATTCCAATGCTGCCT
ATGACAAATTCCAGGACAAGAGAGTGGGGACAAAAGGTCTTGATTTCTCAGATCGTATTGGAAAAACCAAGAGGACAGGA
TATGAATCTGGAGATTATGAGATGTTTGGAGAAGGTCTGGGAGTGAAGGAGACACCTCAGCAAAAGTACCAATGACTGCT
ACATGAAGTCCAAGAGCTGACAACTGAAGTTGAGAAAATTAAGACAACAGTGAAGGAGTCAGCCACTGAGAAGAAGCTGA
CCCCGGTGGTGCTGGCTAAACAGCCGACAGCCCTGAAGCAACAGCTGGTTGCTTCCCACCTGGAAAAGCTGCTCGGACCA
GATGCTGCGATCAACCTCACTGACCCTGATGGAGCTCTTGCTAAGCGCCTACTGCTGCAGCTGGAAGCAACTAAGAACAG
CAAAGGGATTTCAGGGGAAAAGACTGCAAGTGGAACACCTTCAGATAGCAACCTTGTCACTTATGAACTACATTCTCGGC
CTGAACAGGACAATTTCTCTCAAGCTGCCAAAGTTGCCGAACTTGAGAAGCACCTGACAGAGCTGGGGGCAACTGCACGC
TGTGATCGGGATGCTCAGAATCCCCTTTCTGCAGGTCTACAGGGAGCCTGTCTTATGGAAACTGTAGAGCTTTTGCAGGC
AAAGGTGAGCGCTCGGGACCTTGCAGTTTTGGACCAAGTAGAGGCTCGGCTACAGAGTGTCCTTGGAAAGGTGAATGAGA
TCGCCAAGCATAAAGCCTCTGAGCTGGTGCAGAGACTTGTTACCATCAAGCAGATACATGAG

Alignment

ORF - retro_dord_441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAQLEELTSTSVEHIIVNPNAAYDKFKDKRVGTKGLD
          MADPKYA.LP.I.RNEPDVYETS.LPEDDQAEFDA..EEL.STSVEHIIVN.NAAYDKF.DKRVGTKGLD
Retrocopy MADPKYAGLPVIVRNEPDVYETSYLPEDDQAEFDA--EELSSTSVEHIIVNSNAAYDKFQDKRVGTKGLD

Parental  FSDRIGKTKRTGYESGDYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVEKIKTTVKESATEEKLTPVVL
          FSDRIGKTKRTGYESGDYEM.GEGLGVKETPQQKYQ.LLHEVQELTTEVEKIKTTVKESATE.KLTPVVL
Retrocopy FSDRIGKTKRTGYESGDYEMFGEGLGVKETPQQKYQ*LLHEVQELTTEVEKIKTTVKESATEKKLTPVVL

Parental  AKQLTALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATKNSKGISGGKTASGIPSDSNLVTY
          AKQ.TALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATKNSKGISG.KTASG.PSDSNLVTY
Retrocopy AKQPTALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATKNSKGISGEKTASGTPSDSNLVTY

Parental  ELHSRPEQDKFSQAAKVAELEKRLTELEATVRCDQDAQNPLSAGLQGACLMETVELLQAKVSALDLAVLD
          ELHSRPEQD.FSQAAKVAELEK.LTEL.AT.RCD.DAQNPLSAGLQGACLMETVELLQAKVSA.DLAVLD
Retrocopy ELHSRPEQDNFSQAAKVAELEKHLTELGATARCDRDAQNPLSAGLQGACLMETVELLQAKVSARDLAVLD

Parental  QVEARLQSVLGKVNEIAKHKAS--VEDADTQSKVHQ
          QVEARLQSVLGKVNEIAKHKAS..V....T....H.
Retrocopy QVEARLQSVLGKVNEIAKHKASELVQRLVTIKQIHE

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_441 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000233	3 retrocopies	retro_cfam_1095, retro_cfam_385, retro_cfam_579,
Dipodomys ordii	ENSDORG00000007137	1 retrocopy	retro_dord_441 ,
Loxodonta africana	ENSLAFG00000013538	1 retrocopy	retro_lafr_312,
Mustela putorius furo	ENSMPUG00000001840	1 retrocopy	retro_mputfur_197,
Procavia capensis	ENSPCAG00000016236	1 retrocopy	retro_pcap_430,