RetrogeneDB ID:

retro_hsap_2122

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:84517827..84518395(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000182814
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FUNDC2
Ensembl ID:ENSG00000165775
Aliases:None
Description:FUN14 domain containing 2 [Source:HGNC Symbol;Acc:24925]


Retrocopy-Parental alignment summary:






>retro_hsap_2122
ATGGAAACATCTGCCCCACGTGCAGGAAGCCGGGTGGTGGCCACGACAGCGCGCCACTCCGCAGCGTAACCTCGCAGATC
CCCTGCGTGTGTCCTCGCAAGACTAGCTCACCGAAATGGCCGCGTCCAGTCAAGGAAACTTTGAGGGAGATATTGAGTCA
GTGGACCTTGCAGAATTTGCTAAGCAGCAGCCGTGGTGGCGTAAGCTGTTTGGGCCAGAATCTGGACTCTCAGCCGAAAA
GTATAGCGTGGCAACCCACCTGTTCATTGGAGGTGTCACTGGATGGTGCACGGGTTTTATATTCCAGAAGGTTGGAAAGT
TGGCTGCAACAGCTGTGGGAGGTGGATTTTTTCTCCTTCAGCTTGCAAACCATTCTGGGTACATCAAAGTTGATTGGCAA
CGAGTGGAGAAGGACATGAAGAAAGCCAAAGAGCAGCTGAAGATCCCTAAGAGCACTCAGATACCTAACCAGGTCAGGAG
CAAAGCTGAGGAGGTGGTGTCATTTGTGAAGAAAAATGTTCTAGTGACTGGGGGATTTTTCGGAGGCTTTCTGCTTGGCA
TGGCATCC

ORF - retro_hsap_2122 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.53 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMETSAPRAGSQVVATTARHSAA-YRADPLRVSSRDKLTEMAASSQGNFEGNFESLDLAEFAKKQPWWRKL
METSAPRAGS.VVATTARHSAA...ADPLRVSS.D.LTEMAASSQGNFEG..ES.DLAEFAK.QPWWRKL
RetrocopyMETSAPRAGSRVVATTARHSAA>NLADPLRVSSQD*LTEMAASSQGNFEGDIESVDLAEFAKQQPWWRKL
ParentalFGQESGPSAEKYSVATQLFIGGVTGWCTGFIFQKVGKLAATAVGGGFFLLQLANHTGYIKVDWQRVEKDM
FG.ESG.SAEKYSVAT.LFIGGVTGWCTGFIFQKVGKLAATAVGGGFFLLQLANH.GYIKVDWQRVEKDM
RetrocopyFGPESGLSAEKYSVATHLFIGGVTGWCTGFIFQKVGKLAATAVGGGFFLLQLANHSGYIKVDWQRVEKDM
ParentalKKAKEQLKIRKSNQIPTEVRSKAEEVVSFVKKNVLVTGGFFGGFLLGMAS
KKAKEQLKI.KS.QIP..VRSKAEEVVSFVKKNVLVTGGFFGGFLLGMAS
RetrocopyKKAKEQLKIPKSTQIPNQVRSKAEEVVSFVKKNVLVTGGFFGGFLLGMAS

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 44 .98 RPM
bodymap2_adrenal 0 .00 RPM 85 .17 RPM
bodymap2_brain 0 .00 RPM 43 .53 RPM
bodymap2_breast 0 .00 RPM 63 .89 RPM
bodymap2_colon 0 .00 RPM 87 .75 RPM
bodymap2_heart 0 .00 RPM 123 .45 RPM
bodymap2_kidney 0 .00 RPM 72 .90 RPM
bodymap2_liver 0 .00 RPM 38 .55 RPM
bodymap2_lung 0 .00 RPM 66 .70 RPM
bodymap2_lymph_node 0 .00 RPM 80 .84 RPM
bodymap2_ovary 0 .00 RPM 96 .92 RPM
bodymap2_prostate 0 .00 RPM 78 .20 RPM
bodymap2_skeletal_muscle 0 .00 RPM 57 .15 RPM
bodymap2_testis 4 .77 RPM 85 .27 RPM
bodymap2_thyroid 0 .13 RPM 99 .22 RPM
bodymap2_white_blood_cells 0 .49 RPM 38 .12 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2122 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_2122 retrocopy
EST ID Start End Identity Match Mis-match Score
DB079965 84517834 84518072 100 238 0 238

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1255931799 libraries23 libraries4 libraries1 library2 libraries

The graphical summary, for retro_hsap_2122 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2122 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2122 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000169771 retrocopy
retro_btau_292,
Choloepus hoffmanni ENSCHOG0000000430611 retrocopies
retro_chof_1501, retro_chof_161, retro_chof_1640, retro_chof_1674, retro_chof_2087, retro_chof_2351, retro_chof_2355, retro_chof_2396, retro_chof_2491, retro_chof_2519, retro_chof_580,
Callithrix jacchus ENSCJAG000000042873 retrocopies
retro_cjac_1977, retro_cjac_2387, retro_cjac_651,
Dipodomys ordii ENSDORG000000131561 retrocopy
retro_dord_597,
Echinops telfairi ENSETEG000000138172 retrocopies
retro_etel_1724, retro_etel_435,
Homo sapiens ENSG000000695091 retrocopy
retro_hsap_936,
Homo sapiens ENSG00000165775 3 retrocopies
retro_hsap_2122 , retro_hsap_2560, retro_hsap_3530,
Loxodonta africana ENSLAFG000000152891 retrocopy
retro_lafr_2,
Myotis lucifugus ENSMLUG000000077761 retrocopy
retro_mluc_219,
Macaca mulatta ENSMMUG000000102481 retrocopy
retro_mmul_78,
Monodelphis domestica ENSMODG000000164841 retrocopy
retro_mdom_1736,
Mus musculus ENSMUSG000000311982 retrocopies
retro_mmus_2241, retro_mmus_2242,
Nomascus leucogenys ENSNLEG000000144435 retrocopies
retro_nleu_1512, retro_nleu_1662, retro_nleu_1958, retro_nleu_2386, retro_nleu_494,
Otolemur garnettii ENSOGAG000000334613 retrocopies
retro_ogar_1146, retro_ogar_132, retro_ogar_762,
Pongo abelii ENSPPYG000000208974 retrocopies
retro_pabe_1884, retro_pabe_2646, retro_pabe_2916, retro_pabe_49,
Pan troglodytes ENSPTRG000000418524 retrocopies
retro_ptro_1490, retro_ptro_1553, retro_ptro_2254, retro_ptro_2398,
Pteropus vampyrus ENSPVAG000000135521 retrocopy
retro_pvam_210,
Rattus norvegicus ENSRNOG000000240662 retrocopies
retro_rnor_1648, retro_rnor_2870,
Sus scrofa ENSSSCG000000128171 retrocopy
retro_sscr_274,
Ictidomys tridecemlineatus ENSSTOG000000078012 retrocopies
retro_itri_1157, retro_itri_1399,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 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 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 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 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 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 .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 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 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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