RetrogeneDB ID:

retro_hsap_2599

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:46877225..46877633(-)
Located in intron of:ENSG00000075275
Retrocopy
information
Ensembl ID:ENSG00000230634
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM136A
Ensembl ID:ENSG00000035141
Aliases:None
Description:family with sequence similarity 136, member A [Source:HGNC Symbol;Acc:25911]


Retrocopy-Parental alignment summary:






>retro_hsap_2599
GAGCTGCAGCAGCTGCGGGTGCAGGAGGTGGTGGACTCCATGGTGAAGAGTCTGGAGAGAGAGAACATCTGGAAGATGCA
TTGTCTCATGTTCTGGTGCAGCACCAGCTGTTGTGAGGACAGTCAGGCCTCCACGGAGCAGGTGCACCAGTGCATCGAGT
GCCACCATGTGCCTCTGGCTTAAGCCCAGGCTTTGATCACCAGTGAGCTGGAGAAGTTCCAGGACCACCTGGTCCGGTGC
ACCACGCATTGCAACGACAAAGCCAAAGATTCAATAGATGCTGGGAGTAAGGAGCTTCAGTTGAAGCAGAAGCTGGAAGG
TGGTGTGACCAAGTGTGTGGATGACCACATGCACCTGCTCCCAACTATGACCGAGAAGGTGAAGGAGGCTCTCTCATCCA
TTGGGAAA

ORF - retro_hsap_2599 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.62 %
Parental protein coverage: 98.55 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalELQQLRVQEAVESMVKSLERENIRKMQGLMFRCSASCCEDSQASMKQVHQCIERCHVPLAQAQALVTSEL
ELQQLRVQE.V.SMVKSLERENI.KM..LMF.CS.SCCEDSQAS..QVHQCIE..HVPLA.AQAL.TSEL
RetrocopyELQQLRVQEVVDSMVKSLERENIWKMHCLMFWCSTSCCEDSQASTEQVHQCIECHHVPLA*AQALITSEL
ParentalEKFQDRLARCTMHCNDKAKDSIDAGSKELQVKQQLDSCVTKCVDDHMHLIPTMTKKMKEALLSIGK
EKFQD.L.RCT.HCNDKAKDSIDAGSKELQ.KQ.L...VTKCVDDHMHL.PTMT.K.KEAL.SIGK
RetrocopyEKFQDHLVRCTTHCNDKAKDSIDAGSKELQLKQKLEGGVTKCVDDHMHLLPTMTEKVKEALSSIGK

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 16 .10 RPM
bodymap2_adrenal 0 .00 RPM 26 .24 RPM
bodymap2_brain 0 .00 RPM 14 .72 RPM
bodymap2_breast 0 .00 RPM 26 .30 RPM
bodymap2_colon 0 .00 RPM 32 .04 RPM
bodymap2_heart 0 .00 RPM 13 .40 RPM
bodymap2_kidney 0 .00 RPM 38 .26 RPM
bodymap2_liver 0 .00 RPM 23 .98 RPM
bodymap2_lung 0 .00 RPM 9 .07 RPM
bodymap2_lymph_node 0 .00 RPM 26 .39 RPM
bodymap2_ovary 0 .00 RPM 26 .41 RPM
bodymap2_prostate 0 .00 RPM 32 .22 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .93 RPM
bodymap2_testis 0 .00 RPM 23 .81 RPM
bodymap2_thyroid 0 .00 RPM 31 .50 RPM
bodymap2_white_blood_cells 0 .00 RPM 20 .08 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2599 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2599 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2599 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2599 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2599 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1523
Gorilla gorilla retro_ggor_1625
Pongo abelii retro_pabe_1917
Macaca mulatta retro_mmul_656
Parental genes homology:
Parental genes homology involve 18 parental genes, and 73 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000159921 retrocopy
retro_amel_1454,
Bos taurus ENSBTAG000000086742 retrocopies
retro_btau_37, retro_btau_88,
Canis familiaris ENSCAFG000000033532 retrocopies
retro_cfam_1042, retro_cfam_148,
Cavia porcellus ENSCPOG000000091171 retrocopy
retro_cpor_221,
Dasypus novemcinctus ENSDNOG000000194477 retrocopies
retro_dnov_2036, retro_dnov_2465, retro_dnov_2612, retro_dnov_324, retro_dnov_620, retro_dnov_873, retro_dnov_901,
Felis catus ENSFCAG000000081191 retrocopy
retro_fcat_1459,
Homo sapiens ENSG00000035141 5 retrocopies
retro_hsap_1855, retro_hsap_2599 , retro_hsap_2683, retro_hsap_3136, retro_hsap_3413,
Gorilla gorilla ENSGGOG000000232476 retrocopies
retro_ggor_1361, retro_ggor_1625, retro_ggor_2155, retro_ggor_2356, retro_ggor_53, retro_ggor_8,
Macropus eugenii ENSMEUG000000157918 retrocopies
retro_meug_1126, retro_meug_1351, retro_meug_1545, retro_meug_167, retro_meug_2131, retro_meug_219, retro_meug_457, retro_meug_719,
Macaca mulatta ENSMMUG000000079625 retrocopies
retro_mmul_1421, retro_mmul_1772, retro_mmul_220, retro_mmul_327, retro_mmul_656,
Monodelphis domestica ENSMODG000000115331 retrocopy
retro_mdom_65,
Mus musculus ENSMUSG000000574972 retrocopies
retro_mmus_240, retro_mmus_3101,
Pongo abelii ENSPPYG000000123236 retrocopies
retro_pabe_1512, retro_pabe_1917, retro_pabe_2297, retro_pabe_2618, retro_pabe_2828, retro_pabe_3032,
Pan troglodytes ENSPTRG000000120306 retrocopies
retro_ptro_1237, retro_ptro_1523, retro_ptro_1809, retro_ptro_2120, retro_ptro_2318, retro_ptro_3063,
Rattus norvegicus ENSRNOG000000162731 retrocopy
retro_rnor_1679,
Sus scrofa ENSSSCG000000264466 retrocopies
retro_sscr_1075, retro_sscr_229, retro_sscr_230, retro_sscr_309, retro_sscr_335, retro_sscr_914,
Tupaia belangeri ENSTBEG000000174188 retrocopies
retro_tbel_1377, retro_tbel_1875, retro_tbel_2479, retro_tbel_2516, retro_tbel_3373, retro_tbel_3703, retro_tbel_401, retro_tbel_999,
Tursiops truncatus ENSTTRG000000011985 retrocopies
retro_ttru_1110, retro_ttru_1771, retro_ttru_1903, retro_ttru_396, retro_ttru_550,

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 .00 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 .03 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 .00 RPM

Indel association:

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





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