RetrogeneDB ID:

retro_ocun_614

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:13:63292328..63293138(+)
Located in intron of:ENSOCUG00000002011
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KATNBL1
Ensembl ID:ENSOCUG00000017654
Aliases:None
Description:katanin p80 subunit B-like 1 [Source:HGNC Symbol;Acc:26199]


Retrocopy-Parental alignment summary:






>retro_ocun_614
AAGAACATGAAGGAGGTTAAGAAATCTCCCAAACATTTGGCTGCTTACATAAACAGAACAGTTGGACAAGCTGCGAAAAC
CCCAGATAAACTACATAAGGTGATCTATCGCAGAAAGAAAGTTCATCATCCCTTTCCAAATCCTTGTTACAGAAAAAAAC
AGTCCCCTAGCACTGGGGGCTGTGACATGGCAAATAAAGAAAATGAACTGGCTTGTGCAGGTCACCTGCCTGAAAAATTA
CACCATGATAGTCACACATATTTGGTTAATTCCAGTGACCCTGGCTCTTCACAGACAGAAAGCCCATCATCAAAATATAG
TAGTTTTTTTTCTGAGGTTTCTCAGGACCATGAAACAATGGCCCAGGTTTTATTCAGCAGGAATTTGCGATTGAATGTAG
CTTTAACTTTCTGGAAAAAGAGAAGCATAAGTGAACTTGTAGCCTATTTGGTGAGGATAGAAGATCTTGGAGTTGTAGTA
GATTGCCTACCTGTACTCACCAATAGTTTACAGGAAGAAAGACACTATATCTCACTTGGCTGCTGCGTGGACTTGTTGCC
TCTAGTAAAGTCATTACTTCAAAGCAGATTTTAAGAATATGTAATAGTTGGTTTAAACTGGCTTCAAGCAGTCATAAAAA
GGTGGGGGTCAGAACTGTCATCCAAATCAGAAATCAGAAATGATGGAAATATTTAGATTTTAAGACAACAATTAAGTGGG
CTGTGGGAACAAGAAAACCATCTTACTTTGGTTCCAGGATATACTGGTAATATAGCTAAGGATGTAGATGCTTATTTATT
ACAGTTGCAT

ORF - retro_ocun_614 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.3 %
Parental protein coverage: 88.82 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKNMKEVKKSPKHLAAYINRTVGQAVKTPDKLRKVIYRRKKVHHPFPNPCYRKKQSPSTGGCDMANKENEL
KNMKEVKKSPKHLAAYINRTVGQA.KTPDKL.KVIYRRKKVHHPFPNPCYRKKQSPSTGGCDMANKENEL
RetrocopyKNMKEVKKSPKHLAAYINRTVGQAAKTPDKLHKVIYRRKKVHHPFPNPCYRKKQSPSTGGCDMANKENEL
ParentalACAGHLPEKLRHDSRTYLVNSSDPGSSQTESPSSKYSSFFSEVSQDHETMAQVLFSRNLRLNVALTFWRK
ACAGHLPEKL.HDS.TYLVNSSDPGSSQTESPSSKYSSFFSEVSQDHETMAQVLFSRNLRLNVALTFW.K
RetrocopyACAGHLPEKLHHDSHTYLVNSSDPGSSQTESPSSKYSSFFSEVSQDHETMAQVLFSRNLRLNVALTFWKK
ParentalRSISELVAYLVRIEDLGVVVDCLPVLTNSLQEEKHYISLGCCVDLLPLVKSLLKSRFEEYVIVGLNWLQA
RSISELVAYLVRIEDLGVVVDCLPVLTNSLQEE.HYISLGCCVDLLPLVKSLL.SRF.EYVIVGLNWLQA
RetrocopyRSISELVAYLVRIEDLGVVVDCLPVLTNSLQEERHYISLGCCVDLLPLVKSLLQSRF*EYVIVGLNWLQA
ParentalVIKRWWSELSSKSEIRNDGNIQILRQQLSGLWEQENHLTLVPGYTGNIAKDVDAYLLQLH
VIKRW.SELSSKSEIRNDGNI.ILRQQLSGLWEQENHLTLVPGYTGNIAKDVDAYLLQLH
RetrocopyVIKRWGSELSSKSEIRNDGNI*ILRQQLSGLWEQENHLTLVPGYTGNIAKDVDAYLLQLH

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
SRP017611_brain 0 .06 RPM 2 .21 RPM
SRP017611_kidney 0 .10 RPM 3 .85 RPM
SRP017611_liver 0 .00 RPM 1 .85 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_614 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_614 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_614 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000064132 retrocopies
retro_btau_1198, retro_btau_1776,
Callithrix jacchus ENSCJAG000000211103 retrocopies
retro_cjac_1971, retro_cjac_265, retro_cjac_2971,
Cavia porcellus ENSCPOG000000111532 retrocopies
retro_cpor_1374, retro_cpor_1410,
Dasypus novemcinctus ENSDNOG000000162795 retrocopies
retro_dnov_1586, retro_dnov_2201, retro_dnov_2253, retro_dnov_248, retro_dnov_957,
Dipodomys ordii ENSDORG000000131722 retrocopies
retro_dord_378, retro_dord_730,
Equus caballus ENSECAG000000234501 retrocopy
retro_ecab_841,
Echinops telfairi ENSETEG000000016407 retrocopies
retro_etel_1169, retro_etel_1341, retro_etel_2032, retro_etel_2062, retro_etel_319, retro_etel_518, retro_etel_635,
Homo sapiens ENSG000001341523 retrocopies
retro_hsap_3171, retro_hsap_3677, retro_hsap_425,
Gorilla gorilla ENSGGOG000000142303 retrocopies
retro_ggor_1347, retro_ggor_2486, retro_ggor_415,
Macropus eugenii ENSMEUG000000156104 retrocopies
retro_meug_1035, retro_meug_1899, retro_meug_1900, retro_meug_646,
Myotis lucifugus ENSMLUG000000015322 retrocopies
retro_mluc_214, retro_mluc_633,
Macaca mulatta ENSMMUG000000000131 retrocopy
retro_mmul_2005,
Mustela putorius furoENSMPUG000000080191 retrocopy
retro_mputfur_1258,
Nomascus leucogenys ENSNLEG000000107722 retrocopies
retro_nleu_1020, retro_nleu_2679,
Oryctolagus cuniculus ENSOCUG00000017654 5 retrocopies
retro_ocun_1065, retro_ocun_343, retro_ocun_614 , retro_ocun_877, retro_ocun_975,
Otolemur garnettii ENSOGAG000000156333 retrocopies
retro_ogar_1643, retro_ogar_2219, retro_ogar_3301,
Ochotona princeps ENSOPRG000000103791 retrocopy
retro_opri_446,
Pongo abelii ENSPPYG000000063092 retrocopies
retro_pabe_2634, retro_pabe_646,
Pan troglodytes ENSPTRG000000068773 retrocopies
retro_ptro_2271, retro_ptro_2491, retro_ptro_323,
Sorex araneus ENSSARG000000078911 retrocopy
retro_sara_345,
Ictidomys tridecemlineatus ENSSTOG000000038131 retrocopy
retro_itri_1292,
Tupaia belangeri ENSTBEG000000016147 retrocopies
retro_tbel_1267, retro_tbel_127, retro_tbel_1362, retro_tbel_2139, retro_tbel_3276, retro_tbel_4552, retro_tbel_984,
Tarsius syrichta ENSTSYG000000110591 retrocopy
retro_tsyr_2135,
Vicugna pacos ENSVPAG000000071701 retrocopy
retro_vpac_632,


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