RetrogeneDB ID:

retro_hsap_4840

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:62519128..62519548(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230823
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX1
Ensembl ID:ENSG00000108468
Aliases:CBX1, CBX, HP1-BETA, HP1Hs-beta, HP1Hsbeta, M31, MOD1, p25beta
Description:chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]


Retrocopy-Parental alignment summary:






>retro_hsap_4840
GGAAAAAAACTAAACAAGAAGAAAGTGGAGGAAGTGCTAGAAGAGGAGGAAAAGGAATATGTGGTGGAAAAATTTCTCGA
CCGTGGAGTGGTAAAGGACAAAGTGGAGTACCTCCTAAAGTGGAAGGGATTCTCAGATGAGGATAACACATGGGAGCCAG
AAGAGAACCTGGATTGCCTCGACCTCATTGCTGAGTTTCTGCAGTCACAGAAAACAGCACATGAGACAGATAAATCAGAG
GGAGGCAAGCACAAAGCTGATTCTGATTCTGAAGATAAGGGAGAGGAGAGCAAACCAAAGGGGAAGAAAGAAGAGTCAGA
AAAGCCACGAGGCTTTGCTCGAGGTTTGGAGCCAGAGCGGATTATTGGAGCTACAGACTCCAGTGGAGAGGTCATGTTCC
TGATGAAATGGAAAAACTCA

ORF - retro_hsap_4840 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.57 %
Parental protein coverage: 80.46 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQ
GKK.NKKKVEEVLEEEE.EYVVEK.LDR.VVK.KVEYLLKWKGFSDEDNTWEPEENLDC.DLIAEFLQSQ
RetrocopyGKKLNKKKVEEVLEEEEKEYVVEKFLDRGVVKDKVEYLLKWKGFSDEDNTWEPEENLDCLDLIAEFLQSQ
ParentalKTAHETDKSEGGKRKADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMKWKNS
KTAHETDKSEGGK.KADSDSEDKGEESKPK.KKEESEKPRGFARGLEPERIIGATDSSGE.MFLMKWKNS
RetrocopyKTAHETDKSEGGKHKADSDSEDKGEESKPKGKKEESEKPRGFARGLEPERIIGATDSSGEVMFLMKWKNS

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 .00 RPM 30 .25 RPM
bodymap2_adrenal 0 .12 RPM 39 .22 RPM
bodymap2_brain 0 .19 RPM 114 .41 RPM
bodymap2_breast 0 .00 RPM 37 .53 RPM
bodymap2_colon 0 .00 RPM 74 .29 RPM
bodymap2_heart 0 .00 RPM 30 .59 RPM
bodymap2_kidney 0 .00 RPM 48 .23 RPM
bodymap2_liver 0 .00 RPM 10 .52 RPM
bodymap2_lung 0 .00 RPM 41 .63 RPM
bodymap2_lymph_node 0 .00 RPM 48 .35 RPM
bodymap2_ovary 0 .17 RPM 131 .45 RPM
bodymap2_prostate 0 .00 RPM 79 .60 RPM
bodymap2_skeletal_muscle 0 .00 RPM 41 .43 RPM
bodymap2_testis 0 .02 RPM 161 .06 RPM
bodymap2_thyroid 0 .00 RPM 59 .64 RPM
bodymap2_white_blood_cells 0 .00 RPM 64 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4840 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4840 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4840 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4840 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4840 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_3019
Parental genes homology:
Parental genes homology involve 18 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000048902 retrocopies
retro_amel_1228, retro_amel_54,
Canis familiaris ENSCAFG000000168321 retrocopy
retro_cfam_804,
Choloepus hoffmanni ENSCHOG000000119572 retrocopies
retro_chof_1860, retro_chof_2185,
Callithrix jacchus ENSCJAG000000075322 retrocopies
retro_cjac_191, retro_cjac_51,
Felis catus ENSFCAG000000060561 retrocopy
retro_fcat_514,
Homo sapiens ENSG000000949161 retrocopy
retro_hsap_2811,
Homo sapiens ENSG00000108468 3 retrocopies
retro_hsap_4654, retro_hsap_4790, retro_hsap_4840 ,
Homo sapiens ENSG000001225659 retrocopies
retro_hsap_1071, retro_hsap_1145, retro_hsap_1902, retro_hsap_2332, retro_hsap_2771, retro_hsap_3368, retro_hsap_3650, retro_hsap_766, retro_hsap_910,
Gorilla gorilla ENSGGOG000000240633 retrocopies
retro_ggor_2887, retro_ggor_3019, retro_ggor_330,
Microcebus murinus ENSMICG000000095104 retrocopies
retro_mmur_1324, retro_mmur_178, retro_mmur_467, retro_mmur_999,
Mustela putorius furoENSMPUG000000153021 retrocopy
retro_mputfur_1457,
Nomascus leucogenys ENSNLEG000000024354 retrocopies
retro_nleu_1089, retro_nleu_1105, retro_nleu_1955, retro_nleu_2961,
Oryctolagus cuniculus ENSOCUG000000080213 retrocopies
retro_ocun_177, retro_ocun_442, retro_ocun_55,
Procavia capensis ENSPCAG000000023812 retrocopies
retro_pcap_134, retro_pcap_308,
Pongo abelii ENSPPYG000000088911 retrocopy
retro_pabe_78,
Sarcophilus harrisii ENSSHAG000000081921 retrocopy
retro_shar_76,
Sus scrofa ENSSSCG000000175291 retrocopy
retro_sscr_635,
Tupaia belangeri ENSTBEG0000001493139 retrocopies
retro_tbel_1388, retro_tbel_1557, retro_tbel_1613, retro_tbel_1655, retro_tbel_1663, retro_tbel_1794, retro_tbel_2124, retro_tbel_2130, retro_tbel_2281, retro_tbel_2313, retro_tbel_2346, retro_tbel_2539, retro_tbel_2559, retro_tbel_2571, retro_tbel_2587, retro_tbel_270, retro_tbel_2713, retro_tbel_2716, retro_tbel_2752, retro_tbel_2809, retro_tbel_2835, retro_tbel_2854, retro_tbel_2926, retro_tbel_2993, retro_tbel_303, retro_tbel_3236, retro_tbel_3370, retro_tbel_3685, retro_tbel_3998, retro_tbel_4032, retro_tbel_4202, retro_tbel_4611, retro_tbel_4630, retro_tbel_484, retro_tbel_558, retro_tbel_687, retro_tbel_792, retro_tbel_793, retro_tbel_938,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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





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