RetrogeneDB ID:

retro_hsap_901

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:77626038..77626455(-)
Located in intron of:ENSG00000087884
Retrocopy
information
Ensembl ID:ENSG00000255115
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM162B
Ensembl ID:ENSG00000183807
Aliases:FAM162B, C6orf189, bA86F4.2
Description:family with sequence similarity 162, member B [Source:HGNC Symbol;Acc:21549]


Retrocopy-Parental alignment summary:






>retro_hsap_901
TGTGCCCCTGGGAAGCCTCTAGAAGCCACACAGAGGCCCATAGCAACTCTCATGCCCTGGAGGGTCTCACCAGCCACTCC
AGTGATGGGCCCCCCAGTAGCTCTGGGACCCAAGCAGGGATGATTCACAAAGTCCCTACCTAGCACAGGCCTTCACAGTT
CAACAAGAAAATCCTACTGTTGACTGGATTTTTAAAAATCAGTGGAGGAGATCACACTAGAAATGATAGATACTGCAAGA
AACAAAGCTTGAGTGAAAGCTTGTTACCGTAATGAATGGACTCACACATATCACTGCTTTGCAGTGATAGCATCAGCCAA
AAGGGCTGCAGAACATGAATCGTTAACAAGTTGAAATATGTCAAAGATGGCTGTGTGGTGTGAAGAAGCTGCATTAGCTG
CACAGGCTAAGCCTAAA

ORF - retro_hsap_901 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.77 %
Parental protein coverage: 88.89 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalCGPGAPLEATRRP-APALPPR-GLPCYSSGGAPSNSGPQGHGEIHRVPTQRRPSQFDKKILLWTGRFK-S
C.PG.PLEAT.RP.A...P.R.GL...SS.G.PS.SG.Q..G.IH.VPT..RPSQF.KKILL.TG..K.S
RetrocopyCAPGKPLEATQRPIATLMPWR<GLTSHSSDGPPSSSGTQA-GMIHKVPT*HRPSQFNKKILLLTGFLK>S
ParentalMEEIPPRIPPEMIDTARNKARVKACY-IMIGLTIIA-CFAVIVSAKRAVERHESLTSWNLAKKAKWREEA
.EE....I..EMIDTARNKA.VKACY..M.GLT.I..CFAVI.SAKRA.E.HESLTS.N..K.A.W.EEA
RetrocopyVEE----ITLEMIDTARNKA*VKACY>VMNGLTHIT<CFAVIASAKRAAE-HESLTS*NMSKMAVWCEEA
ParentalALAAQAKAK
ALAAQAK.K
RetrocopyALAAQAKPK

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 4 .21 RPM
bodymap2_adrenal 0 .00 RPM 7 .45 RPM
bodymap2_brain 0 .00 RPM 1 .38 RPM
bodymap2_breast 0 .00 RPM 3 .42 RPM
bodymap2_colon 0 .00 RPM 6 .54 RPM
bodymap2_heart 0 .15 RPM 2 .62 RPM
bodymap2_kidney 0 .00 RPM 2 .61 RPM
bodymap2_liver 0 .00 RPM 0 .02 RPM
bodymap2_lung 0 .00 RPM 15 .72 RPM
bodymap2_lymph_node 0 .00 RPM 8 .88 RPM
bodymap2_ovary 0 .15 RPM 3 .57 RPM
bodymap2_prostate 0 .10 RPM 6 .72 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .46 RPM
bodymap2_testis 0 .00 RPM 3 .79 RPM
bodymap2_thyroid 0 .08 RPM 2 .07 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_901 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_901 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_901 retrocopy 5' end.

Lab - click to see more details

retro_hsap_901 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_901 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_621
Parental genes homology:
Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000183807 2 retrocopies
retro_hsap_3744, retro_hsap_901 ,
Gorilla gorilla ENSGGOG000000020451 retrocopy
retro_ggor_728,
Microcebus murinus ENSMICG000000145551 retrocopy
retro_mmur_746,
Mus musculus ENSMUSG000000199091 retrocopy
retro_mmus_2292,
Pan troglodytes ENSPTRG000000185384 retrocopies
retro_ptro_2541, retro_ptro_2542, retro_ptro_2994, retro_ptro_621,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 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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