RetrogeneDB ID:

retro_shar_348

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL841420.1:992846..993269(-)
Located in intron of:ENSSHAG00000012186
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000008347
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_348
ATGGGTAAGTGTCAAGGTTTTTATGCAGCTAAAAAGCTCCAAAACCACAGAAGAGACCAAAAATAGCATAATAAATGATA
GAAGAAAGCTCATGCAGGTACTGCCTTGAAGGTCAACCTATGTGGAGAAGCATCCCATACAAAAGGGATTGTCTTAGAAA
AAGTTGGTGTGGAAGTCAAGCAGCCCAATTCTGCCATCAGGAAGTATATGAGAGTCTAGCTGATTAAGAATGACAAAAAA
AAAATCACTGTCTTTGTTCCCAATATTGGTTGTTTGAATTTTATTGAGGAAAGTGACATAGTTTTGGTTGCTGGATTTGT
TCAAAAAAGTCATAATATTTCTAAAGTGTGTTTCAAGGTTGTAAAAGTTGCAAATGTTTCTCTTCTGGTCTTTTGCAAAG
GCAAGAAGGAAAGATCAAGATCA

ORF - retro_shar_348 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.44 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCV
MGKC.G...A.KL..HRRDQK.H.K..KKAH.GTALK.N..G.ASH.KGIVLEKVGVE.KQPNSAIRK..
RetrocopyMGKCQGFYAAKKLQNHRRDQK*HNK**KKAHAGTALKVNLCGEASHTKGIVLEKVGVEVKQPNSAIRKYM
ParentalRVQLIKN-GKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKE
RV.LIKN.....T.FVPN.GCLNFIEE.D.VLVAGF..K.H....I..V.FKVVKVANVSLL...KGKKE
RetrocopyRV*LIKNDXXXXTVFVPNIGCLNFIEESDIVLVAGFVQKSH---NISKVCFKVVKVANVSLLVFCKGKKE
ParentalRPRS
R.RS
RetrocopyRSRS

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






RNA-Seq - click to see more details

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST - click to see more details

Sarcophilus harrisii was not studied using EST data.

TSS - click to see more details

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab - click to see more details

retro_shar_348 was not experimentally validated.

Retrocopy orthology:
Sarcophilus harrisii 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 34 parental genes, and 153 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000111361 retrocopy
retro_acar_85,
Ailuropoda melanoleuca ENSAMEG000000159663 retrocopies
retro_amel_1096, retro_amel_341, retro_amel_751,
Bos taurus ENSBTAG000000133583 retrocopies
retro_btau_173, retro_btau_205, retro_btau_80,
Canis familiaris ENSCAFG000000308967 retrocopies
retro_cfam_1145, retro_cfam_1305, retro_cfam_1415, retro_cfam_1743, retro_cfam_2105, retro_cfam_375, retro_cfam_436,
Callithrix jacchus ENSCJAG000000112472 retrocopies
retro_cjac_126, retro_cjac_256,
Cavia porcellus ENSCPOG000000227052 retrocopies
retro_cpor_1182, retro_cpor_1377,
Dipodomys ordii ENSDORG000000018132 retrocopies
retro_dord_187, retro_dord_93,
Equus caballus ENSECAG000000205232 retrocopies
retro_ecab_275, retro_ecab_500,
Erinaceus europaeus ENSEEUG000000018497 retrocopies
retro_eeur_102, retro_eeur_262, retro_eeur_326, retro_eeur_462, retro_eeur_515, retro_eeur_53, retro_eeur_662,
Felis catus ENSFCAG000000088397 retrocopies
retro_fcat_1557, retro_fcat_1601, retro_fcat_1876, retro_fcat_2000, retro_fcat_5, retro_fcat_609, retro_fcat_644,
Homo sapiens ENSG000001864686 retrocopies
retro_hsap_1778, retro_hsap_2940, retro_hsap_3107, retro_hsap_3287, retro_hsap_3989, retro_hsap_4697,
Gorilla gorilla ENSGGOG000000250146 retrocopies
retro_ggor_1316, retro_ggor_2038, retro_ggor_2131, retro_ggor_2237, retro_ggor_2677, retro_ggor_286,
Loxodonta africana ENSLAFG000000315063 retrocopies
retro_lafr_1117, retro_lafr_1216, retro_lafr_606,
Macropus eugenii ENSMEUG000000129311 retrocopy
retro_meug_811,
Microcebus murinus ENSMICG000000139642 retrocopies
retro_mmur_1354, retro_mmur_872,
Myotis lucifugus ENSMLUG000000139392 retrocopies
retro_mluc_1676, retro_mluc_2183,
Macaca mulatta ENSMMUG000000035784 retrocopies
retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Monodelphis domestica ENSMODG000000202553 retrocopies
retro_mdom_1518, retro_mdom_1612, retro_mdom_395,
Mustela putorius furoENSMPUG000000081141 retrocopy
retro_mputfur_1298,
Mus musculus ENSMUSG0000004951712 retrocopies
retro_mmus_2151, retro_mmus_2200, retro_mmus_2690, retro_mmus_2812, retro_mmus_3118, retro_mmus_3163, retro_mmus_3168, retro_mmus_323, retro_mmus_3619, retro_mmus_365, retro_mmus_836, retro_mmus_848,
Nomascus leucogenys ENSNLEG000000132033 retrocopies
retro_nleu_1353, retro_nleu_1909, retro_nleu_764,
Oryctolagus cuniculus ENSOCUG000000103632 retrocopies
retro_ocun_195, retro_ocun_95,
Otolemur garnettii ENSOGAG0000000816311 retrocopies
retro_ogar_1177, retro_ogar_1303, retro_ogar_1785, retro_ogar_1849, retro_ogar_238, retro_ogar_2479, retro_ogar_253, retro_ogar_2695, retro_ogar_2823, retro_ogar_3519, retro_ogar_364,
Pongo abelii ENSPPYG000000156087 retrocopies
retro_pabe_1538, retro_pabe_1585, retro_pabe_19, retro_pabe_2515, retro_pabe_2567, retro_pabe_2716, retro_pabe_3129,
Pan troglodytes ENSPTRG000000170526 retrocopies
retro_ptro_1190, retro_ptro_2056, retro_ptro_2223, retro_ptro_2707, retro_ptro_3075, retro_ptro_3122,
Pteropus vampyrus ENSPVAG000000020834 retrocopies
retro_pvam_1483, retro_pvam_782, retro_pvam_80, retro_pvam_922,
Rattus norvegicus ENSRNOG0000001658012 retrocopies
retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sorex araneus ENSSARG000000089048 retrocopies
retro_sara_194, retro_sara_346, retro_sara_422, retro_sara_481, retro_sara_540, retro_sara_647, retro_sara_648, retro_sara_714,
Sarcophilus harrisii ENSSHAG00000008347 2 retrocopies
retro_shar_257, retro_shar_348 ,
Sus scrofa ENSSSCG000000141331 retrocopy
retro_sscr_92,
Ictidomys tridecemlineatus ENSSTOG000000008243 retrocopies
retro_itri_1418, retro_itri_204, retro_itri_377,
Tarsius syrichta ENSTSYG000000113855 retrocopies
retro_tsyr_1656, retro_tsyr_1946, retro_tsyr_406, retro_tsyr_462, retro_tsyr_933,
Tursiops truncatus ENSTTRG000000144916 retrocopies
retro_ttru_1253, retro_ttru_1555, retro_ttru_186, retro_ttru_458, retro_ttru_487, retro_ttru_578,
Vicugna pacos ENSVPAG000000094277 retrocopies
retro_vpac_195, retro_vpac_239, retro_vpac_393, retro_vpac_543, retro_vpac_56, retro_vpac_598, retro_vpac_81,




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