RetrogeneDB ID:

retro_shar_813

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL865283.1:38540..39101(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C1QBP
Ensembl ID:ENSSHAG00000002441
Aliases:None
Description:complement component 1, q subcomponent binding protein [Source:HGNC Symbol;Acc:1243]


Retrocopy-Parental alignment summary:






>retro_shar_813
AAGGAGACGAAAATGTAGAAACACAAACATCTTTCCAAGATGTCAGGAGACTGGGAACTGGCTGTGCAAGGGACAGAAGC
CAAGTTTGTCTGGTGATTAGCTGGAAAAAGTTCATGGTCACATTCAATATTAACAGCATCCCACCTATATTTGACGATGA
GCCATCAGAATGACAGAAAGGACAAAAACAGCAAGAGACTGAACTTCTGTCCCTCCAGTTTATCTTGCTGGTTGCAGGTT
GTGAAGAATGATACCAAGAATAGCATTGTGTTGCACCATCACTGATCCAGAACATGAGGTTGGACAGGAAAAAGAGATTG
AGAATGGCATTTTCTTCACCTCGGAAGTGTGCTTTCAGTCCACCAGCTGGTCAGACTGGAAGGATACAAACTACACTCTA
TGTACAGATTCCCTGAAATGGCCCCTGTATGATCATTTGGTCTTCCTGGGTAACTGAGGGTGAAAAATACATTAGCAGAT
GAACAGATCCAGCTCAGCATGGCCTTAGAACACTAAGAATACATCAACTTTCTGGAAACTCTGAAAGGGTTTGCCAAGTG
T

ORF - retro_shar_813 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.14 %
Parental protein coverage: 82.53 %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalEERKIQKHKSLPKMSGDWELAVQGTEAKLTRKLAGE-KITVTFNINNSIPPTFDDEPSSEGQKGQEEQEP
.E.K..KHK.L.KMSGDWELAVQGTEAK....LAG..K..VTFNIN.SIPP.FDDEPS............
RetrocopyKETKM*KHKHLSKMSGDWELAVQGTEAKFVW*LAGK<KFMVTFNIN-SIPPIFDDEPSE*QKGQKQQETE
ParentalELT-STPNFVVEVIKNDTQKALVLDCH-YPEDEVGQEEEEESDIFSIREVSFQPTSESDWKDTNYTLNTD
.L..S.......V.KNDT....VL..H..PE.EVGQE.E.E..IF...EV.FQ.TS.SDWKDTNYTL.TD
RetrocopyLLS>SSLSCWLQVVKNDTKNSIVLHHH>DPEHEVGQEKEIENGIFFTSEVCFQSTSWSDWKDTNYTLCTD
ParentalSLDWALYDHLMDFLADRG-VDNTFADELIELSTALEHQEYINFLEDLKGFVKC
SL.W.LYDHL..FL...G.V.NT.ADE.I.LS.ALEH.EYINFLE.LKGF.KC
RetrocopySLKWPLYDHLV-FLGN*G<VKNTLADEQIQLSMALEH*EYINFLETLKGFAKC

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_813 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 17 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000060432 retrocopies
retro_amel_1734, retro_amel_356,
Canis familiaris ENSCAFG000000155423 retrocopies
retro_cfam_1595, retro_cfam_319, retro_cfam_325,
Callithrix jacchus ENSCJAG000000113526 retrocopies
retro_cjac_2041, retro_cjac_2408, retro_cjac_4033, retro_cjac_604, retro_cjac_680, retro_cjac_946,
Dasypus novemcinctus ENSDNOG000000088873 retrocopies
retro_dnov_1151, retro_dnov_1946, retro_dnov_702,
Felis catus ENSFCAG000000264743 retrocopies
retro_fcat_1135, retro_fcat_1763, retro_fcat_892,
Homo sapiens ENSG000001085612 retrocopies
retro_hsap_1475, retro_hsap_2516,
Gorilla gorilla ENSGGOG000000027455 retrocopies
retro_ggor_1133, retro_ggor_1569, retro_ggor_3007, retro_ggor_3008, retro_ggor_717,
Macropus eugenii ENSMEUG0000001488213 retrocopies
retro_meug_1068, retro_meug_1347, retro_meug_1363, retro_meug_1446, retro_meug_1901, retro_meug_1940, retro_meug_1970, retro_meug_2069, retro_meug_2128, retro_meug_434, retro_meug_580, retro_meug_988, retro_meug_989,
Macaca mulatta ENSMMUG000000065921 retrocopy
retro_mmul_1554,
Mustela putorius furoENSMPUG000000112461 retrocopy
retro_mputfur_1213,
Nomascus leucogenys ENSNLEG000000090812 retrocopies
retro_nleu_2379, retro_nleu_3038,
Otolemur garnettii ENSOGAG000000016105 retrocopies
retro_ogar_1376, retro_ogar_2502, retro_ogar_2518, retro_ogar_2879, retro_ogar_768,
Ochotona princeps ENSOPRG000000131501 retrocopy
retro_opri_408,
Pongo abelii ENSPPYG000000078706 retrocopies
retro_pabe_1222, retro_pabe_1385, retro_pabe_1413, retro_pabe_1866, retro_pabe_1868, retro_pabe_670,
Pan troglodytes ENSPTRG000000086313 retrocopies
retro_ptro_1140, retro_ptro_1461, retro_ptro_998,
Pteropus vampyrus ENSPVAG000000024661 retrocopy
retro_pvam_384,
Sarcophilus harrisii ENSSHAG00000002441 2 retrocopies
retro_shar_620, retro_shar_813 ,


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