RetrogeneDB ID:

retro_dord_709

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_59354:5754..6236(+)
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_709
GAGGAAGAGGAAAATGTGGCAGAAAAAGTTCTCCACCATCAAGTTGTAAAAGGCAAAGTGGAATACCTCCTAAGCGGAAG
GGTTTGTCAAATGAGGACAATACATGGGAGCCAGAAGGCAACCTACATTGCCCCTACCTCACTGTTGAGTTTAGTCTCAG
AAAATAGCACAAGAAACAGAAGTCAGAGGGAGGTAAGTGTAAAGCTGATTATGATTCTGAAGATATATGGAGAGGAAAGC
AAACCAAAGAAGACATAAGAGTTAGGTAAGTCACAAGGCTTTTCTCCGGTTTGGAGCCGGAGCCAATTACAGGAGCTACA
GACTCCAGTGGAGAGCTCATGTTACTGATGAAATGGATGAACTCTGATGACGCTGATCTATCAAGTTCCTGACAAGGAAG
CCAATGTCAAGTGCCCACAGGCTGTGTCAGATCCTTCAGTGAAGAAAGGTTGACGTGGCATTCCTACCCCTCAGAGGATG
AC

ORF - retro_dord_709 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.87 %
Parental protein coverage: 87.57 %
Number of stop codons detected: 3
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalEEEEYVVEKVLDRRVVKGKVEYLL-KWKGFSDEDNTWEPEENLDCPDLIAEFLQSQKTAHETDKSEGGKR
EEEE.V.EKVL...VVKGKVEYLL.K.KG.S.EDNTWEPE.NL.CP.L..EF..S....H...KSEGGK.
RetrocopyEEEENVAEKVLHHQVVKGKVEYLL<KRKGLSNEDNTWEPEGNLHCPYLTVEF--SLRK*HKKQKSEGGKC
ParentalKADSDSED-KGEESKPKKKKEESEKPRGFA-RGLEPERIIGATDSSGELMFLMKWKNSDEADLVPA-KEA
KAD.DSED..GEESKPKK..E...K..GF...GLEPE.I.GATDSSGELM.LMKW.NSD.ADL.......
RetrocopyKADYDSED>YGEESKPKKT*ELG-KSQGFS<SGLEPEPITGATDSSGELMLLMKWMNSDDADLSSS*QGS
ParentalNVKCPQVVISFYEE-RLTWHSYPSEDD
....P........E.RLTWHSYPSEDD
RetrocopyQCQVPTGCVRSFSEERLTWHSYPSEDD

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






RNA-Seq - click to see more details

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Dipodomys ordii was not studied using ChIP-Seq data.

EST - click to see more details

Dipodomys ordii was not studied using EST data.

TSS - click to see more details

Dipodomys ordii was not studied using FANTOM5 data.

Lab - click to see more details

retro_dord_709 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
retro_amel_1228, retro_amel_54,
Bos taurus ENSBTAG000000029499 retrocopies
retro_btau_1121, retro_btau_1394, retro_btau_148, retro_btau_1583, retro_btau_1615, retro_btau_550, retro_btau_558, retro_btau_714, retro_btau_807,
Callithrix jacchus ENSCJAG000000075322 retrocopies
retro_cjac_191, retro_cjac_51,
Dipodomys ordii ENSDORG00000000716 2 retrocopies
retro_dord_594, retro_dord_709 ,
Dipodomys ordii ENSDORG0000000548711 retrocopies
retro_dord_309, retro_dord_405, retro_dord_437, retro_dord_440, retro_dord_456, retro_dord_502, retro_dord_629, retro_dord_630, retro_dord_655, retro_dord_700, retro_dord_780,
Erinaceus europaeus ENSEEUG000000048743 retrocopies
retro_eeur_121, retro_eeur_228, retro_eeur_396,
Echinops telfairi ENSETEG000000002037 retrocopies
retro_etel_1083, retro_etel_1572, retro_etel_1577, retro_etel_1611, retro_etel_2165, retro_etel_382, retro_etel_932,
Felis catus ENSFCAG000000060561 retrocopy
retro_fcat_514,
Myotis lucifugus ENSMLUG000000050302 retrocopies
retro_mluc_1000, retro_mluc_1533,
Mus musculus ENSMUSG000000186661 retrocopy
retro_mmus_3108,
Oryctolagus cuniculus ENSOCUG000000080213 retrocopies
retro_ocun_177, retro_ocun_442, retro_ocun_55,
Otolemur garnettii ENSOGAG000000056589 retrocopies
retro_ogar_1087, retro_ogar_1092, retro_ogar_1322, retro_ogar_2056, retro_ogar_2396, retro_ogar_2443, retro_ogar_2840, retro_ogar_2880, retro_ogar_368,
Ochotona princeps ENSOPRG000000036991 retrocopy
retro_opri_552,
Pongo abelii ENSPPYG000000088911 retrocopy
retro_pabe_78,
Rattus norvegicus ENSRNOG000000086892 retrocopies
retro_rnor_2388, retro_rnor_2841,
Sarcophilus harrisii ENSSHAG000000081921 retrocopy
retro_shar_76,
Ictidomys tridecemlineatus ENSSTOG000000239863 retrocopies
retro_itri_1282, retro_itri_1599, retro_itri_1867,
Tarsius syrichta ENSTSYG000000047692 retrocopies
retro_tsyr_1672, retro_tsyr_467,


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