RetrogeneDB ID:

retro_hsap_850

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:14695149..14696101(-)
Located in intron of:ENSG00000152270
Retrocopy
information
Ensembl ID:ENSG00000255040
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_850
ATGGCTTCAAAACAGGACCCAAAGCCTAAATTCCAGGAGGTTGAGTGAGTGCTGTGCTTTCATGGGCCTCTTCTTCATGA
AACAAAGTGTGTAAAGGTTGCCATTAAGGACAAACAAGTGAAATACTTTATACATTACAGTGGTTGGAATAAAAATTGGG
ATGAGTGGGTTCCAGAGAGCAGAGTACTCAAATACAAGGACACTAATTTGCAGAAAGAATAAGAACTTCAAAAAGCCAAT
CAGGAGCAGTATGCAGAGGGGAAGACGATAGGGGCTGCCCCAGGAAAGAAGACATCTGGTCTCCAACAGAAAAATGTTGA
AGTGAAAACAAAAAAGAACAAACAGAAAACCCCTGGAAATGGAGATGGTGGCAGTACCAGTGAGACTCCTTGGCCTCCTC
GGAAGAAAAGGACCCGGGTAGATCCTACTGTTGAAAATGAGGAAACATTCATGAACAGAGTTGAAGTTAAAGTAAAGCTT
CCTGAAGAGCTAAAACTGTGGCTTGTTGATGACTGGGACTTAATTACCAGACGAAAACAGCTCTTTTAACTTCCTGCCAA
GAAGAAATGTGGATTCCATTCTTGAGGATTACGCAAATTACAAGAAATCTGGTGGAAACACAGATAATAAGGAGTATGCG
GTTAATGAAGTTGTGGCAGGGATAAAAGAATACTTCAACGTAATGTTGGGCACCCAACTACTCTACAAATTTGAGAGACC
ACAGTATGCCGAAATTCTTGCAGATCACCCCAAGGCACCCATGTCCCAGGTGTATGGAGTGCCACATCTCCTGAGATTAC
TTGTACGAATTGGAGCAATGTTGGCCTATACACCTCTGGATGAGAAGAGCCTTGCTTAATTACTGAATTATCTTCATGAT
TTCCTGAAGTACCTGGCAAAGAATTCTACAACTTTGTTTAGTGCCAGAGATTATGAAGTGGCTCCTCCTGAG

ORF - retro_hsap_850 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.42 %
Parental protein coverage: 98.14 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
MA.KQDPKPKFQE.E.VLCFHGPLL.E.KCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKY.DTNL
RetrocopyMASKQDPKPKFQEVE*VLCFHGPLLHETKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYKDTNL
ParentalQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRARV
QK..ELQKANQEQYAEGK..GAAPGKKTSGL................PGNGDGGSTSETP.PPRKKR.RV
RetrocopyQKE*ELQKANQEQYAEGKTIGAAPGKKTSGLXXXXXXXXXXXXXXXXPGNGDGGSTSETPWPPRKKRTRV
ParentalDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKK-NVDSILEDYANYKKSRGNTDN
DPTVENEETFMNRVEVKVK.PEELK.WLVDDWDLITR.KQLF.LPAKK.NVDSILEDYANYKKS.GNTDN
RetrocopyDPTVENEETFMNRVEVKVKLPEELKLWLVDDWDLITRRKQLF*LPAKK>NVDSILEDYANYKKSGGNTDN
ParentalKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPL
KEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHP.APMSQVYG.PHLLRL.VRIGAMLAYTPL
RetrocopyKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPKAPMSQVYGVPHLLRLLVRIGAMLAYTPL
ParentalDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPE
DEKSLA.LLNYLHDFLKYLAKNS.TLFSA.DYEVAPPE
RetrocopyDEKSLA*LLNYLHDFLKYLAKNSTTLFSARDYEVAPPE

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 403 .50 RPM
bodymap2_adrenal 0 .04 RPM 314 .53 RPM
bodymap2_brain 0 .00 RPM 505 .20 RPM
bodymap2_breast 0 .00 RPM 354 .28 RPM
bodymap2_colon 0 .02 RPM 440 .61 RPM
bodymap2_heart 0 .11 RPM 229 .42 RPM
bodymap2_kidney 0 .00 RPM 281 .27 RPM
bodymap2_liver 0 .04 RPM 94 .40 RPM
bodymap2_lung 0 .00 RPM 367 .95 RPM
bodymap2_lymph_node 0 .00 RPM 255 .39 RPM
bodymap2_ovary 0 .00 RPM 497 .94 RPM
bodymap2_prostate 0 .00 RPM 338 .07 RPM
bodymap2_skeletal_muscle 0 .00 RPM 209 .69 RPM
bodymap2_testis 0 .13 RPM 608 .48 RPM
bodymap2_thyroid 0 .00 RPM 443 .38 RPM
bodymap2_white_blood_cells 0 .00 RPM 243 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_850 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_850 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_850 retrocopy 5' end.

Lab - click to see more details

retro_hsap_850 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_850 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_591
Gorilla gorilla retro_ggor_694
Pongo abelii retro_pabe_695
Macaca mulatta retro_mmul_1064
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 = 0.09 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 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 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 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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