RetrogeneDB ID:

retro_hsap_2185

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:180678977..180679399(+)
Located in intron of:ENSG00000144331
Retrocopy
information
Ensembl ID:ENSG00000213126
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TXNL4A
Ensembl ID:ENSG00000141759
Aliases:TXNL4A, DIB1, DIM1, HsT161, SNRNP15, TXNL4, U5-15kD
Description:thioredoxin-like 4A [Source:HGNC Symbol;Acc:30551]


Retrocopy-Parental alignment summary:






>retro_hsap_2185
ATGTCACACATGCTCCTGCACCTCCACAGCAGCTGGCAGGTGGACCAGGCCATCCTCCCAGGAGAGGACTGCATGGCTGT
CATTCGCTTCGGCCACGGCTGGGACCCCACATGCATGAAAATGGATAAGGTCTTGTACAGCATCATTGAGAAGGTTAAAG
ATTTTGCAGTTATTTTTCTTGTGAATATTACCAAAGTACCTGACTTCAACAAAATGTATGAGTTATATGATCCATGCACT
ATCATGTTTTTCTTCAGGAACAAGCACATCATGGTTGTCTTGGGGACTGGCAACAACAAGATTAACTGGGCCATGGAGGA
CAAGCAGGAGATGGTCGACATCATAGAGACCGTGGACTGTAGGGCCCTCAATGGTGGCGACCTGGTCTTGTCCCCAAAAA
CTACTCCACCAAGTCCAGATAC

ORF - retro_hsap_2185 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.32 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFN
MS.ML.HLH..WQVDQAIL..ED...VIRFGH.WDPTCMKMD.VLYSI.EKVK.FAVI.LV.IT.VPDFN
RetrocopyMSHMLLHLHSSWQVDQAILPGEDCMAVIRFGHGWDPTCMKMDKVLYSIIEKVKDFAVIFLVNITKVPDFN
ParentalKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVS-PKDYSTK
KMYELYDPCT.MFFFRNKHIM..LGTG.NNKINWAMEDKQEMVDIIETV...A..G..LV.S.PK.YSTK
RetrocopyKMYELYDPCTIMFFFRNKHIMVVLGTG-NNKINWAMEDKQEMVDIIETVDCRALNGGDLVLS<PKNYSTK
ParentalYRY
.RY
RetrocopySRY

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 28 .58 RPM
bodymap2_adrenal 0 .04 RPM 40 .88 RPM
bodymap2_brain 0 .00 RPM 47 .16 RPM
bodymap2_breast 0 .00 RPM 37 .78 RPM
bodymap2_colon 0 .00 RPM 32 .56 RPM
bodymap2_heart 0 .00 RPM 17 .17 RPM
bodymap2_kidney 0 .00 RPM 29 .57 RPM
bodymap2_liver 0 .00 RPM 21 .90 RPM
bodymap2_lung 0 .00 RPM 24 .72 RPM
bodymap2_lymph_node 0 .00 RPM 30 .96 RPM
bodymap2_ovary 0 .00 RPM 23 .17 RPM
bodymap2_prostate 0 .00 RPM 22 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 21 .32 RPM
bodymap2_testis 0 .00 RPM 43 .98 RPM
bodymap2_thyroid 0 .00 RPM 34 .99 RPM
bodymap2_white_blood_cells 0 .00 RPM 27 .09 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2185 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2185 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2185 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2185 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2185 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1731
Macaca mulatta retro_mmul_913
Parental genes homology:
Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000101302 retrocopies
retro_cjac_2805, retro_cjac_3659,
Homo sapiens ENSG00000141759 2 retrocopies
retro_hsap_2185 , retro_hsap_4900,
Gorilla gorilla ENSGGOG000000052852 retrocopies
retro_ggor_1731, retro_ggor_3060,
Loxodonta africana ENSLAFG000000031901 retrocopy
retro_lafr_198,
Myotis lucifugus ENSMLUG000000091881 retrocopy
retro_mluc_562,
Macaca mulatta ENSMMUG000000016132 retrocopies
retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys ENSNLEG000000083782 retrocopies
retro_nleu_1268, retro_nleu_314,
Otolemur garnettii ENSOGAG000000347531 retrocopy
retro_ogar_1751,
Pan troglodytes ENSPTRG000000101361 retrocopy
retro_ptro_1663,
Rattus norvegicus ENSRNOG000000175962 retrocopies
retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus ENSSTOG000000222771 retrocopy
retro_itri_1063,
Tarsius syrichta ENSTSYG000000094281 retrocopy
retro_tsyr_240,

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 = 0.02 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 .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 .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 .00 RPM

Indel association:

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





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