RetrogeneDB ID:

retro_hsap_3415

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:3941513..3941951(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000217566
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TDGF1
Ensembl ID:ENSG00000241186
Aliases:TDGF1, CR, CRGF, CRIPTO
Description:teratocarcinoma-derived growth factor 1 [Source:HGNC Symbol;Acc:11701]


Retrocopy-Parental alignment summary:






>retro_hsap_3415
AGTGTAATTTTGATCATGGCCATTTCAAGGCATTTGAAACGGGATTCGTTGCCGGGTTGGGCCACCATGAACTTGCACAG
TCACCTCAGGAGGCCGAGCCTTCAGAGATGACAGCATTCAGCCTCAGGAGGAGCCTGCAATTCACCCACGGTCTTCCCAG
TATATCCCTTCCATGGGGATACAAGACAGTAAGGAGCTAAACAGAACCTGCTGTCTGAATGGGGAACCTGCATGCTGGGG
TTCTTTTGTGTCTGAGCCCTGTCCTTCTATGGACAGACCTGTGAATATTACATGCACAATGAGAGCCGTAGGTTTGAGCC
CCGTGACACCCAGCTGTCCAAGAAGTGTTCCCTGTGTAAATGCTGACATGGACAGCTCCGCTGCTTGCCTCAGGCATTTC
TACCTGGGTGTGACGGCCTTGTGATGGACAAGCACCTC

ORF - retro_hsap_3415 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.67 %
Parental protein coverage: 78.19 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSVIWIMAIS-KVFELGLVAGLGHQEFARPSR-GYLAFRDDSIWPQEEPAIRPRSSQRVPPMGIQHSKELN
SVI.IMAIS.K.FE.G.VAGLGH.E.A.....G..AFRDDSI.PQEEPAI.PRSSQ..P.MGIQ.SKELN
RetrocopySVILIMAIS<KAFETGFVAGLGHHELAQSPQ<GGRAFRDDSIQPQEEPAIHPRSSQYIPSMGIQDSKELN
ParentalRTCCLNG-GTCMLGSFCACPPSFYGRNCEHDVRKENCGSVPHDTWLPKKCSLCKCWHGQLRCFPQAFLPG
RTCCLNG.GTCMLG.FC....SFYG..CE.....E.....P.DT.L.KKCSLCKC.HGQLRC.PQAFLPG
RetrocopyRTCCLNG<GTCMLGFFCV*ALSFYGQTCEYYMHNESRRFEPRDTQLSKKCSLCKC*HGQLRCLPQAFLPG
ParentalCDGLVMDEHL
CDGLVMD.HL
RetrocopyCDGLVMDKHL

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 0 .46 RPM
bodymap2_adrenal 0 .04 RPM 0 .18 RPM
bodymap2_brain 0 .00 RPM 0 .21 RPM
bodymap2_breast 0 .00 RPM 0 .39 RPM
bodymap2_colon 0 .00 RPM 1 .86 RPM
bodymap2_heart 0 .00 RPM 0 .96 RPM
bodymap2_kidney 0 .00 RPM 19 .73 RPM
bodymap2_liver 0 .00 RPM 1 .22 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 1 .50 RPM
bodymap2_ovary 0 .00 RPM 10 .16 RPM
bodymap2_prostate 0 .00 RPM 0 .24 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .29 RPM
bodymap2_testis 0 .06 RPM 3 .64 RPM
bodymap2_thyroid 0 .00 RPM 1 .71 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_3415 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3415 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3415 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3415 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3415 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2319
Gorilla gorilla retro_ggor_2307
Macaca mulatta retro_mmul_1744
Parental genes homology:
Parental genes homology involve 14 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000021743 retrocopies
retro_cjac_1594, retro_cjac_4151, retro_cjac_938,
Felis catus ENSFCAG000000145081 retrocopy
retro_fcat_714,
Homo sapiens ENSG00000241186 7 retrocopies
retro_hsap_1999, retro_hsap_2393, retro_hsap_2709, retro_hsap_3415 , retro_hsap_3956, retro_hsap_4737, retro_hsap_4804,
Gorilla gorilla ENSGGOG000000034535 retrocopies
retro_ggor_1447, retro_ggor_1815, retro_ggor_2307, retro_ggor_2943, retro_ggor_2990,
Loxodonta africana ENSLAFG000000091404 retrocopies
retro_lafr_1037, retro_lafr_1067, retro_lafr_757, retro_lafr_871,
Microcebus murinus ENSMICG000000164921 retrocopy
retro_mmur_635,
Macaca mulatta ENSMMUG000000030886 retrocopies
retro_mmul_1744, retro_mmul_2290, retro_mmul_2560, retro_mmul_742, retro_mmul_770, retro_mmul_967,
Mustela putorius furoENSMPUG000000151671 retrocopy
retro_mputfur_961,
Mus musculus ENSMUSG000000324943 retrocopies
retro_mmus_1429, retro_mmus_1544, retro_mmus_1908,
Nomascus leucogenys ENSNLEG000000061436 retrocopies
retro_nleu_1649, retro_nleu_2124, retro_nleu_2179, retro_nleu_2317, retro_nleu_2519, retro_nleu_535,
Otolemur garnettii ENSOGAG000000170391 retrocopy
retro_ogar_2611,
Pan troglodytes ENSPTRG000000148547 retrocopies
retro_ptro_1333, retro_ptro_1749, retro_ptro_1831, retro_ptro_2319, retro_ptro_2685, retro_ptro_3153, retro_ptro_3194,
Tarsius syrichta ENSTSYG000000136092 retrocopies
retro_tsyr_295, retro_tsyr_574,
Tursiops truncatus ENSTTRG000000172991 retrocopy
retro_ttru_441,

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 = 0.03 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 .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 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 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 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 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 .00 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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