RetrogeneDB ID:

retro_hsap_3677

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:147124072..147124845(-)
Located in intron of:ENSG00000118492
Retrocopy
information
Ensembl ID:ENSG00000228283
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KATNBL1
Ensembl ID:ENSG00000134152
Aliases:KATNBL1, C15orf29
Description:katanin p80 subunit B-like 1 [Source:HGNC Symbol;Acc:26199]


Retrocopy-Parental alignment summary:






>retro_hsap_3677
ATGGCATCGGAAACTCACAATGTTAAAAAACGGAACTTTTGTAATAAGATTGAGGATCATTTCATTGATCTTCCTAGAAA
AAAAGATCTCTAATTTCACTGATAAGAACATGAAGGAGGTTAAGAAGTCTCCAAAACAGTTGGCTGCTTACATAAATAGA
ACAGTTGGACAAACTGTGAAAAGCCCAGATAAACTTCGTAAAGTGATCTATCGCAGAAAGAAAGTTCATCATCCCTTTCC
AAATCTTTGTTACAGAAAAAAACAGCCCCCTGGAAGGTGGGGGCTGTGACATGGCAAATAAAGAAAATGAACTGGCTTGT
GCAGGCCACCAGACTGAAAAATTACACCATGACAGTCGAACATATTTGGTTAACTCCAGTGATTCTGGTTCTTCACAGAC
AGAAAGCCCATCATCAAAATATAGTGGGTTTTTTTCTGAGGTTTCTCAGGACCATGAAACAATGGTCCAAGTTTTGTTCA
GCAGGAATATGAGATTGAATGTAGCTTTAAGTTTCTGGAGAAGGAGAAGTATAAGTGAACTTGTAGCTTATTTGTTGAGG
ATAGAAGATCTTGGCGTTGTGGTAGATTGCCTTCCTGTGCTCACCAATTGTTTACAGGAAGAAAAACAATATATCTCACT
TGGCTGCTGTGTAGACTTGTTGCTTCTAGTAAAGTCACTACTTAAAAGCAAATTTGAAGAATATGTTATAGTTGGTTTAA
ACTGGCTTCAAGCAGTCATTAAAAGGTGGTGGTCAGAACTATCATCCAAAACA

ORF - retro_hsap_3677 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.37 %
Parental protein coverage: 84.54 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMASETHNVKKRNFCNKIEDHFIDLPRKK-ISNFTNKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI
MASETHNVKKRNFCNKIEDHFIDLPRKK.ISNFT.KNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI
RetrocopyMASETHNVKKRNFCNKIEDHFIDLPRKK>ISNFTDKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI
ParentalYRRKKVHHPFPNPCYRKKQSPG-SGGCDMANKENELACAGHLPEKLHHDSRTYLVNSSDSGSSQTESPSS
YRRKKVHHPFPN.CYRKKQ.PG..GGCDMANKENELACAGH..EKLHHDSRTYLVNSSDSGSSQTESPSS
RetrocopyYRRKKVHHPFPNLCYRKKQPPG>GGGCDMANKENELACAGHQTEKLHHDSRTYLVNSSDSGSSQTESPSS
ParentalKYSGFFSEVSQDHETMAQVLFSRNMRLNVALTFWRKRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEK
KYSGFFSEVSQDHETM.QVLFSRNMRLNVAL.FWR.RSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEK
RetrocopyKYSGFFSEVSQDHETMVQVLFSRNMRLNVALSFWRRRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEK
ParentalQYISLGCCVDLLPLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSKT
QYISLGCCVDLL.LVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSKT
RetrocopyQYISLGCCVDLLLLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSKT

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
bodymap2_adipose 0 .02 RPM 16 .26 RPM
bodymap2_adrenal 0 .02 RPM 23 .87 RPM
bodymap2_brain 0 .00 RPM 23 .42 RPM
bodymap2_breast 0 .00 RPM 27 .92 RPM
bodymap2_colon 0 .00 RPM 19 .86 RPM
bodymap2_heart 0 .00 RPM 13 .20 RPM
bodymap2_kidney 0 .06 RPM 29 .04 RPM
bodymap2_liver 0 .00 RPM 9 .23 RPM
bodymap2_lung 0 .00 RPM 25 .49 RPM
bodymap2_lymph_node 0 .00 RPM 36 .46 RPM
bodymap2_ovary 0 .00 RPM 28 .68 RPM
bodymap2_prostate 0 .00 RPM 28 .98 RPM
bodymap2_skeletal_muscle 0 .00 RPM 4 .80 RPM
bodymap2_testis 0 .21 RPM 27 .15 RPM
bodymap2_thyroid 0 .04 RPM 17 .95 RPM
bodymap2_white_blood_cells 0 .02 RPM 28 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_3677 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 6:147124744..147125089
ENCFF002CXP POLR2A 6:147124676..147125156
ENCFF002CXR POLR2A 6:147124695..147125131
ENCFF002DBE POLR2A 6:147124665..147125161

EST - click to see more details

No EST(s) were mapped for retro_hsap_3677 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3677 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3677 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3677 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2491
Gorilla gorilla retro_ggor_2486
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 ENSG00000134152 3 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 ENSOCUG000000176545 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,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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