RetrogeneDB ID:

retro_dord_594

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_37691:3991..4549(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cbx1
Ensembl ID:ENSDORG00000000716
Aliases:None
Description:chromobox 1 [Source:MGI Symbol;Acc:MGI:105369]


Retrocopy-Parental alignment summary:






>retro_dord_594
ATGGGAAAAAAGCAAAACAAGAAGAAAGTGGAGGAGGTCCTAGAAGAGGAGGAAGAGGAATATGTGGTGGAAAAAGTTCT
TGACCGTCGAGTTATGTAAAGGGCACCGTAGAGTACCTTCTAAAGTGGAAGGGTTTCTCAGATGAGGATAATACATGGGA
GCCAGAAGAGAACCTGGATTGTCCCGACCTCATTGCTGAGTTTCTACAGTCACAGAAAACAGCACGTGAGACAGACAAAT
CAGAGGGAGGCAAGCGTAAAGCTGATTCTGATTCTGAGGATAAGGGAGAGGAAAGCAAACCTAAGAAGAAAGAAAGAAAA
GTCAGAAAAGCCTCAAGGCTTTGCCCGGGGTTTGGAGCTGGAGCAGATTATTGGAGCTACAGACTCCAGCGGAGAGCTCA
TGTTCCTGATGAAATGGAAAGACTCTGATGAGGCTGATCTAGTCCTTGCCAAGGAAGCTAATGTCCAGTGCCCACAGGTT
GTCATATCCTTCTATGGGGAAAGGTTGAAGTGGCATTCCTACCCCTCAGAGGATGACGACAAAAAAGACAACAAGAAT

ORF - retro_dord_594 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.7 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMGKKQNKKKVEEVLEE-EEEEYVVEKVLDRRV-VKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFL
MGKKQNKKKVEEVLEE.EEE..V......R...VKG.VEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFL
RetrocopyMGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVM<VKGTVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFL
ParentalQSQKTAHETDKSEGGKRKADSDSEDKGEESKPKKK-KEESEKPRGFARGLEPERIIGATDSSGELMFLMK
QSQKTA.ETDKSEGGKRKADSDSEDKGEESKPKKK.KE.SEKP.GFARGLE.E.IIGATDSSGELMFLMK
RetrocopyQSQKTARETDKSEGGKRKADSDSEDKGEESKPKKK>KEKSEKPQGFARGLELEQIIGATDSSGELMFLMK
ParentalWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN
WK.SDEADLV.AKEANV.CPQVVISFY.ERL.WHSYPSEDDDKKD.KN
RetrocopyWKDSDEADLVLAKEANVQCPQVVISFYGERLKWHSYPSEDDDKKDNKN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Dipodomys ordii was not studied using RNA-Seq expression data.
Dipodomys ordii was not studied using ChIP-Seq data.
Dipodomys ordii was not studied using EST data.
Dipodomys ordii was not studied using FANTOM5 data.
retro_dord_594 was not experimentally validated.

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.

Parental genes homology:
Parental genes homology involve 18 parental genes, and 62 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000048902 retrocopies
Bos taurus ENSBTAG000000029499 retrocopies
Callithrix jacchus ENSCJAG000000075322 retrocopies
Dipodomys ordii ENSDORG00000000716 2 retrocopies
retro_dord_594 , retro_dord_709,
Dipodomys ordii ENSDORG0000000548711 retrocopies
Erinaceus europaeus ENSEEUG000000048743 retrocopies
Echinops telfairi ENSETEG000000002037 retrocopies
Felis catus ENSFCAG000000060561 retrocopy
Myotis lucifugus ENSMLUG000000050302 retrocopies
Mus musculus ENSMUSG000000186661 retrocopy
Oryctolagus cuniculus ENSOCUG000000080213 retrocopies
Otolemur garnettii ENSOGAG000000056589 retrocopies
Ochotona princeps ENSOPRG000000036991 retrocopy
Pongo abelii ENSPPYG000000088911 retrocopy
Rattus norvegicus ENSRNOG000000086892 retrocopies
Sarcophilus harrisii ENSSHAG000000081921 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000239863 retrocopies
Tarsius syrichta ENSTSYG000000047692 retrocopies



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