RetrogeneDB ID:

retro_dnov_226

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_2733:607387..607912(-)
Located in intron of:ENSDNOG00000014674
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARL5A
Ensembl ID:ENSDNOG00000013331
Aliases:None
Description:ADP-ribosylation factor-like 5A [Source:HGNC Symbol;Acc:696]


Retrocopy-Parental alignment summary:






>retro_dnov_226
GGGAACTCTTTTCCCAGGATATGAGGACTATTCAGTCACCAGGAGCAAAAGGTTATCATTGTTGGGCTGGATAATGCAGG
GAAAACTAATATCCTTTGGGAATTTTCTATGAATGAAGTTATACATACATCCTGTACAATAGGGAGTAATGTCAAAGAGA
TAGTTCTTAATAATACATTTCCTAATGTAGGATGTTGGTGACCAAGAATTTCTTTGTTCTTTCTGGAACACTTACTATAA
TGCTGAAGTTGTAACCGTTGTAGACAGTACAAACAGAGAAAGGATTTCCATAACTGGAGAAGCAACTGTATAAAACATTA
GTACATGAGAACCTAAGAAAATCTGGATTGTATTGGTTTTTGCTAATAAAGATGTTAAGAACGTATGACTGTAGGAGAAA
TCTTCTAGTTTTTTAAACTAACTTCTGTTAAAGATCACCAGTAGAATATCCAGGAATGCTGTGTTCATACAGGCAAGGGA
GTATACCAAGGACTTGAATGGATGATGTCATGATTTAAGATTAGA

ORF - retro_dnov_226 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.84 %
Parental protein coverage: 99.44 %
Number of stop codons detected: 5
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalGILFTRIWRLFNHQEHKVIIVGLDNAGKTTILXXXSMNEVVHTSPTIGSNVEEIVVNNT-RFLMWDIGGQ
G..F.RI..LF.HQE.KVIIVGLDNAGKT.IL...SMNEV.HTS.TIGSNV.E..V.N...FLM.D.G.Q
RetrocopyGNSFPRI*GLFSHQEQKVIIVGLDNAGKTNILWEFSMNEVIHTSCTIGSNVKE-IVLNN>HFLM*DVGDQ
ParentalESLRSSWNTYYTNTEFVIVVVDSTDRERISVTRE-ELYKMLAHEDLRKAGLLIFA-NKQDVK-ECMTVAE
E.L.S.WNTYY.N.E.V..VVDST.RERIS.T.E..LYK.L.HE.LRK.GL..F.....DVK.E.MTV.E
RetrocopyEFLCSFWNTYY-NAE-VVTVVDSTNRERISITGE>QLYKTLVHENLRKSGLYWFL<ANKDVK<ERMTVGE
ParentalISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR
I..F.KLTS.KDHQ..IQ.CC..TG.G..QGLEWMMS..KIR
RetrocopyIF*FFKLTSVKDHQ*NIQECCVHTGKGVYQGLEWMMS*FKIR

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012922_ascending_colon 0 .19 RPM 15 .56 RPM
SRP012922_cerebellum 0 .27 RPM 6 .60 RPM
SRP012922_heart 0 .00 RPM 5 .34 RPM
SRP012922_kidney 0 .00 RPM 6 .57 RPM
SRP012922_liver 0 .00 RPM 4 .18 RPM
SRP012922_lung 0 .46 RPM 10 .39 RPM
SRP012922_quadricep_muscle 0 .00 RPM 10 .73 RPM
SRP012922_spleen 0 .46 RPM 13 .05 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_226 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus 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 23 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000506225 retrocopies
retro_chof_1109, retro_chof_1132, retro_chof_1205, retro_chof_1218, retro_chof_1407, retro_chof_1414, retro_chof_1443, retro_chof_1573, retro_chof_1712, retro_chof_1953, retro_chof_206, retro_chof_2081, retro_chof_2131, retro_chof_2142, retro_chof_2433, retro_chof_2464, retro_chof_2470, retro_chof_2713, retro_chof_373, retro_chof_547, retro_chof_836, retro_chof_857, retro_chof_865, retro_chof_972, retro_chof_98,
Callithrix jacchus ENSCJAG000000033119 retrocopies
retro_cjac_1054, retro_cjac_1111, retro_cjac_1255, retro_cjac_1921, retro_cjac_2949, retro_cjac_3920, retro_cjac_4131, retro_cjac_4175, retro_cjac_4211,
Cavia porcellus ENSCPOG000000052091 retrocopy
retro_cpor_913,
Dasypus novemcinctus ENSDNOG00000013331 16 retrocopies
retro_dnov_105, retro_dnov_1165, retro_dnov_1244, retro_dnov_1953, retro_dnov_2159, retro_dnov_226 , retro_dnov_2265, retro_dnov_2268, retro_dnov_2344, retro_dnov_2394, retro_dnov_563, retro_dnov_671, retro_dnov_713, retro_dnov_811, retro_dnov_818, retro_dnov_881,
Equus caballus ENSECAG000000236721 retrocopy
retro_ecab_1087,
Erinaceus europaeus ENSEEUG000000093503 retrocopies
retro_eeur_240, retro_eeur_642, retro_eeur_699,
Felis catus ENSFCAG000000147422 retrocopies
retro_fcat_569, retro_fcat_65,
Homo sapiens ENSG000001629805 retrocopies
retro_hsap_2549, retro_hsap_4715, retro_hsap_4768, retro_hsap_4894, retro_hsap_721,
Gorilla gorilla ENSGGOG000000020665 retrocopies
retro_ggor_1131, retro_ggor_1594, retro_ggor_2930, retro_ggor_2971, retro_ggor_3056,
Loxodonta africana ENSLAFG000000321044 retrocopies
retro_lafr_1178, retro_lafr_1228, retro_lafr_1244, retro_lafr_599,
Microcebus murinus ENSMICG000000157887 retrocopies
retro_mmur_1271, retro_mmur_1487, retro_mmur_1586, retro_mmur_1618, retro_mmur_468, retro_mmur_652, retro_mmur_923,
Macaca mulatta ENSMMUG000000105215 retrocopies
retro_mmul_2519, retro_mmul_2543, retro_mmul_2630, retro_mmul_616, retro_mmul_641,
Monodelphis domestica ENSMODG000000039781 retrocopy
retro_mdom_75,
Mustela putorius furoENSMPUG000000003962 retrocopies
retro_mputfur_1477, retro_mputfur_352,
Mus musculus ENSMUSG000000360931 retrocopy
retro_mmus_2232,
Nomascus leucogenys ENSNLEG000000111912 retrocopies
retro_nleu_1259, retro_nleu_2280,
Otolemur garnettii ENSOGAG000000114246 retrocopies
retro_ogar_1879, retro_ogar_2112, retro_ogar_2675, retro_ogar_3146, retro_ogar_3465, retro_ogar_728,
Pongo abelii ENSPPYG000000128484 retrocopies
retro_pabe_3711, retro_pabe_3806, retro_pabe_3832, retro_pabe_621,
Pan troglodytes ENSPTRG000000125385 retrocopies
retro_ptro_1486, retro_ptro_3134, retro_ptro_3175, retro_ptro_3262, retro_ptro_514,
Ictidomys tridecemlineatus ENSSTOG000000163261 retrocopy
retro_itri_62,
Tupaia belangeri ENSTBEG000000115118 retrocopies
retro_tbel_1173, retro_tbel_1540, retro_tbel_3202, retro_tbel_3464, retro_tbel_3681, retro_tbel_3835, retro_tbel_4207, retro_tbel_4665,
Tursiops truncatus ENSTTRG000000155642 retrocopies
retro_ttru_1008, retro_ttru_1843,
Vicugna pacos ENSVPAG000000021722 retrocopies
retro_vpac_318, retro_vpac_399,


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