RetrogeneDB ID:

retro_hsap_955

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:7759435..7759929(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000255977
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CLTA
Ensembl ID:ENSG00000122705
Aliases:CLTA, LCA
Description:clathrin, light chain A [Source:HGNC Symbol;Acc:2090]


Retrocopy-Parental alignment summary:






>retro_hsap_955
GACGAGGCCTTCACCATCCTGGAAGGTGGTGCCCCCAGGCCCCAGGCACATGGCAAGCTGGATGCTGTTGATGGAGTAAT
GAATGGTAAATACTACCAGGAAAGTAATAGTCCAACAGACAGTTGTGCAGCATTTCACAAGTGGATAGATTGCAGTCAGA
GCCTGAAAGTATCCGTAAATGGAGAGAAGAGCAAACAGAACGCTTGGAAGCCCTTGATGCCAATTCTCAGAAGCAAGAAG
CAGAGTGGAAAGAAAAGGCAATAAAGGAGCTAGAGGTGTGATATGTGAGATAGGATGAGCAACTACAGAAAACAAAAGCA
AACAGGGCAGCAGAAGAAGCCTTTGTAAATGACATTGACCAGTTCTTCCCAGGCACTGAGTGGGAAAGTGTGGCCTGGCT
GTGTAACTTTAACCCCAAGTCCAGAAGGCAGGCTAAAGACATCTCCCAGAGGTGCTCAGTCCTCATCTCCCTCAAGCAGG
CCCCGCTGGTGCAC

ORF - retro_hsap_955 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.7 %
Parental protein coverage: 77.98 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDEAFAILDGGAPGPQPHGEPPGGPDAVDGVMNGEYYQESNGPTDSYAA-ISQVDRLQSEPESIRKWREEQ
DEAF.IL.GGAP.PQ.H....G..DAVDGVMNG.YYQESN.PTDS.AA.ISQVDRLQSEPESIRKWREEQ
RetrocopyDEAFTILEGGAPRPQAH----GKLDAVDGVMNGKYYQESNSPTDSCAA<ISQVDRLQSEPESIRKWREEQ
ParentalMERLEALDANSRKQEAEWKEKAIKELEEWYARQDEQLQKTKANNRAAEEAFVNDIDESSPGTEWERVARL
.ERLEALDANS.KQEAEWKEKAIKELE..Y.R.DEQLQKTKA.NRAAEEAFVNDID...PGTEWE.VA.L
RetrocopyTERLEALDANSQKQEAEWKEKAIKELEV*YVR*DEQLQKTKA-NRAAEEAFVNDIDQFFPGTEWESVAWL
ParentalCDFNPKSSKQAKDVSRMRSVLISLKQAPLVH
C.FNPKS..QAKD.S...SVLISLKQAPLVH
RetrocopyCNFNPKSRRQAKDISQRCSVLISLKQAPLVH

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 76 .25 RPM
bodymap2_adrenal 0 .00 RPM 93 .07 RPM
bodymap2_brain 0 .00 RPM 97 .00 RPM
bodymap2_breast 0 .00 RPM 74 .98 RPM
bodymap2_colon 0 .00 RPM 93 .88 RPM
bodymap2_heart 0 .00 RPM 19 .86 RPM
bodymap2_kidney 0 .02 RPM 91 .26 RPM
bodymap2_liver 0 .00 RPM 46 .15 RPM
bodymap2_lung 0 .00 RPM 69 .57 RPM
bodymap2_lymph_node 0 .00 RPM 69 .33 RPM
bodymap2_ovary 0 .00 RPM 113 .31 RPM
bodymap2_prostate 0 .00 RPM 101 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .39 RPM
bodymap2_testis 0 .00 RPM 98 .19 RPM
bodymap2_thyroid 0 .00 RPM 104 .17 RPM
bodymap2_white_blood_cells 0 .00 RPM 68 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_955 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_955 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_955 retrocopy 5' end.

Lab - click to see more details

retro_hsap_955 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_955 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_785
Parental genes homology:
Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000011371 retrocopy
retro_btau_327,
Homo sapiens ENSG00000122705 2 retrocopies
retro_hsap_4022, retro_hsap_955 ,
Macropus eugenii ENSMEUG000000108581 retrocopy
retro_meug_480,
Macaca mulatta ENSMMUG000000061322 retrocopies
retro_mmul_2319, retro_mmul_785,
Monodelphis domestica ENSMODG000000026101 retrocopy
retro_mdom_1148,
Nomascus leucogenys ENSNLEG000000038741 retrocopy
retro_nleu_659,
Pongo abelii ENSPPYG000000190691 retrocopy
retro_pabe_3300,
Pan troglodytes ENSPTRG000000209301 retrocopy
retro_ptro_2727,

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 .02 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 .00 RPM

Indel association:

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



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