RetrogeneDB ID:

retro_hsap_309

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:220426911..220427880(+)
Located in intron of:ENSG00000118873
Retrocopy
information
Ensembl ID:ENSG00000218283
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MORF4L1
Ensembl ID:ENSG00000185787
Aliases:MORF4L1, Eaf3, HsT17725, MEAF3, MORFRG15, MRG15, S863-6
Description:mortality factor 4 like 1 [Source:HGNC Symbol;Acc:16989]


Retrocopy-Parental alignment summary:






>retro_hsap_309
ATGGCGCGGAAGCAGGACCCGAAGCCTAAATTCCAGGAGGGTGAGCGAGTGCTGTGCTTTCATGGGCCTCTTCTTTATGA
AGCAAAGTGTGTAAAGGTTGCCATAAAGGACAAACAAGTGAAATACTTCATACATTACAGTGGTTGGAATAAAAATTGGG
ATGAGTGGGTTCCGGAGAGCAGAGTACTCAAATACGTGGACACCAATTTGCAGAAACAGCGAGAACTTCAAAAAGCCAAT
CAGGAGCAGTATGCAGAGGGGAAGATGAGAGGGGCTGCCCCAGGAAAGAAGACATCTGGTCTGCAACAGAAAAATGTTGA
AGTGAAAACGAAAAAGAACAAACAGAAAACACCTGGAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGCCTCCTT
GGAAGAAAAGGGCCCGGGTAGATCCTACTGTTGAAAATGAGGAAACATTCATGAACAGAGTTGAAGTTAAAGTAAAGATT
CCTGAATAGCTAAAACCGTGGCTTGTTGATGACTGGGACTTAATTACCAGGCAAAAACAGCTCTTTTATCTTCCTGCCAA
GAAGAATGTGGATTCCATTCTTGAGGATTATGCAAATTACAAGAAATCTCGTGGAAACACAGATAATAAGGAGTATGCGG
TTAATGAAGTTGTGGCAGGGATAAAAGAATACTTCAACGTAATGTTGGGTACCCAGCTACTCTATAAATTTGAGAGACCA
CAGTATGCCGAAATTCTTGCAGATCATCCCGATGCACCCATGTCCCAGGTGTATGGAGCGCCACATCTCCTGAGATTATT
TGTACGAATTGGAGCAATGTTGGCCTATACACCTCTGGATGAGAAGAGCCTTGCTTTATTACTCAATTATCTTCACGATT
TCCTAAAGTACCTGGCAAAGAATTCTGCAACTTTGTTTAGTGCCAGCGATTATGAAGTGGCTCCTCCTGAGTACCATCGG
AAAGCTGTG

ORF - retro_hsap_309 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.07 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
MA.KQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
RetrocopyMARKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
ParentalQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRARV
QKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPP.KKRARV
RetrocopyQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPWKKRARV
ParentalDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNK
DPTVENEETFMNRVEVKVKIPE.LKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNK
RetrocopyDPTVENEETFMNRVEVKVKIPE*LKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNK
ParentalEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLD
EYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLD
RetrocopyEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLD
ParentalEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
EKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
RetrocopyEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV

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 11 .73 RPM 403 .50 RPM
bodymap2_adrenal 9 .05 RPM 314 .53 RPM
bodymap2_brain 15 .07 RPM 505 .20 RPM
bodymap2_breast 9 .30 RPM 354 .28 RPM
bodymap2_colon 12 .59 RPM 440 .61 RPM
bodymap2_heart 14 .09 RPM 229 .42 RPM
bodymap2_kidney 5 .77 RPM 281 .27 RPM
bodymap2_liver 3 .97 RPM 94 .40 RPM
bodymap2_lung 16 .37 RPM 367 .95 RPM
bodymap2_lymph_node 7 .64 RPM 255 .39 RPM
bodymap2_ovary 15 .69 RPM 497 .94 RPM
bodymap2_prostate 13 .39 RPM 338 .07 RPM
bodymap2_skeletal_muscle 12 .22 RPM 209 .69 RPM
bodymap2_testis 20 .19 RPM 608 .48 RPM
bodymap2_thyroid 15 .10 RPM 443 .38 RPM
bodymap2_white_blood_cells 9 .43 RPM 243 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_309 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_309 retrocopy.

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_89956909 libraries650 libraries256 libraries10 libraries4 libraries
TSS #2 TSS_89957295 libraries448 libraries931 libraries126 libraries29 libraries

The graphical summary, for retro_hsap_309 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_309 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_309 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123441 retrocopy
retro_amel_124,
Bos taurus ENSBTAG000000109881 retrocopy
retro_btau_137,
Canis familiaris ENSCAFG000000141131 retrocopy
retro_cfam_20,
Callithrix jacchus ENSCJAG000000022145 retrocopies
retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Homo sapiens ENSG00000185787 3 retrocopies
retro_hsap_309 , retro_hsap_3125, retro_hsap_850,
Gorilla gorilla ENSGGOG000000168263 retrocopies
retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana ENSLAFG000000098511 retrocopy
retro_lafr_62,
Macaca mulatta ENSMMUG000000229261 retrocopy
retro_mmul_1064,
Monodelphis domestica ENSMODG000000115172 retrocopies
retro_mdom_150, retro_mdom_158,
Mustela putorius furoENSMPUG000000154291 retrocopy
retro_mputfur_180,
Mus musculus ENSMUSG000000622709 retrocopies
retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys ENSNLEG000000086783 retrocopies
retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus ENSOCUG000000151172 retrocopies
retro_ocun_108, retro_ocun_21,
Otolemur garnettii ENSOGAG000000060474 retrocopies
retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii ENSPPYG000000067034 retrocopies
retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes ENSPTRG000000073513 retrocopies
retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus ENSRNOG000000144106 retrocopies
retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sarcophilus harrisii ENSSHAG000000184021 retrocopy
retro_shar_393,
Sus scrofa ENSSSCG000000017691 retrocopy
retro_sscr_93,
Ictidomys tridecemlineatus ENSSTOG000000132943 retrocopies
retro_itri_111, retro_itri_1545, retro_itri_1608,

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 = 18.25 RPM Legend:


Library Retrogene expression
CEU_NA11831 14 .44 RPM
CEU_NA11843 11 .37 RPM
CEU_NA11930 14 .15 RPM
CEU_NA12004 13 .52 RPM
CEU_NA12400 12 .10 RPM
CEU_NA12751 13 .04 RPM
CEU_NA12760 12 .62 RPM
CEU_NA12827 11 .27 RPM
CEU_NA12872 14 .24 RPM
CEU_NA12873 11 .45 RPM
FIN_HG00183 12 .99 RPM
FIN_HG00277 15 .64 RPM
FIN_HG00315 12 .20 RPM
FIN_HG00321 14 .90 RPM
FIN_HG00328 14 .94 RPM
FIN_HG00338 13 .75 RPM
FIN_HG00349 13 .66 RPM
FIN_HG00375 13 .11 RPM
FIN_HG00377 12 .51 RPM
FIN_HG00378 13 .83 RPM
GBR_HG00099 13 .60 RPM
GBR_HG00111 12 .51 RPM
GBR_HG00114 14 .62 RPM
GBR_HG00119 14 .75 RPM
GBR_HG00131 13 .16 RPM
GBR_HG00133 11 .84 RPM
GBR_HG00134 12 .23 RPM
GBR_HG00137 10 .86 RPM
GBR_HG00142 11 .73 RPM
GBR_HG00143 12 .35 RPM
TSI_NA20512 13 .06 RPM
TSI_NA20513 14 .12 RPM
TSI_NA20518 17 .62 RPM
TSI_NA20532 10 .07 RPM
TSI_NA20538 12 .81 RPM
TSI_NA20756 16 .12 RPM
TSI_NA20765 13 .22 RPM
TSI_NA20771 14 .27 RPM
TSI_NA20786 15 .48 RPM
TSI_NA20798 13 .00 RPM
YRI_NA18870 13 .54 RPM
YRI_NA18907 15 .22 RPM
YRI_NA18916 12 .27 RPM
YRI_NA19093 12 .23 RPM
YRI_NA19099 15 .15 RPM
YRI_NA19114 14 .97 RPM
YRI_NA19118 10 .57 RPM
YRI_NA19213 18 .25 RPM
YRI_NA19214 13 .85 RPM
YRI_NA19223 16 .53 RPM

Indel association:

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



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