RetrogeneDB ID:

retro_hsap_3419

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:6535042..6535737(+)
Located in intron of:ENSG00000216863
Retrocopy
information
Ensembl ID:ENSG00000218868
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CNN3
Ensembl ID:ENSG00000117519
Aliases:None
Description:calponin 3, acidic [Source:HGNC Symbol;Acc:2157]


Retrocopy-Parental alignment summary:






>retro_hsap_3419
CAGCTGGGCTTAAAGGAGGGCATCCTCCTCTGTGAACTCATCAACAAGCTGCAGGCAGGCCCAATGAAGAAAGTCAATGA
GTCCTCATTAAACTGGCCTCAGCGGAGAATATTGGCAACTTTATTAAAGCTATTCAGGCTTATGGTGTGAAGCCACGTGA
CATATTTGAAGTAAGTGATCTTTTTAGGATGGAAACGTGACCCAAGTTCAGGCTACTCTGGTGGCCCTAGTAGGTTGGCA
AGCACAAAAGGATACAACCACGGACATCAGGGTTAAATATACAGAAAAACAAACACGACGTTAGGATGAAGGAAAATTAA
AAGCTGCTGAAACTGTAATTGGATTGCGGATGGGAACCAACGAAGTGCCAGCCAGGCAGGTATGTCAGCTTACGGGACTA
CAGGCATCTTTATGATCCCAACATGCAAACTGACAAACGTTTTGACCAGACCACAGTTTGTCTGCAGATGGTCACTAACA
AAGCAGACAGCCAGGCAGGGATGTTAGCACCAGGCACCAGAAGGGCCATCTACTATCAGAAGCTAACATTACAGCCAGTA
GACCACTTGACAATTTCTCTACAGATGGGTACCAACAAAGTGGCTTCCCAGAAAAGAATGGGTGTGCACGGGCTTGGGGG
GCAAGTATATGGTCGCAAATACTGTGCTGCTCTGACAGAAACTATCATTCACAAC

ORF - retro_hsap_3419 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.73 %
Parental protein coverage: 71.43 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalQLGLKDGIILCELINKLQPGSVKKVNESSLNWPQ-LENIGNFIKAIQAYGMKPHDIFEANDLFE-NGNMT
QLGLK.GI.LCELINKLQ.G..KKVNESSLNWPQ..ENIGNFIKAIQAYG.KP.DIFE..DLF...GN.T
RetrocopyQLGLKEGILLCELINKLQAGPMKKVNESSLNWPQ<AENIGNFIKAIQAYGVKPRDIFEVSDLFR<DGNVT
ParentalQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTN-KCASQAGMTAYGTR
QVQ.TLVAL.G....K...TT.DI.VKY.EKQTRR.DEGKLKA...VIGL.MGTN...ASQAGM.AYGT.
RetrocopyQVQATLVALVGWQAQKD--TTTDIRVKYTEKQTRR*DEGKLKAAETVIGLRMGTN<RSASQAGMSAYGTT
Parental-RHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVAS
.RHLYDP.MQTDK.FDQTT..LQM.TNK..SQAGMLAPGTRR.IY.QKLTLQPVD..TISLQMGTNKVAS
Retrocopy<RHLYDPNMQTDKRFDQTTVCLQMVTNKADSQAGMLAPGTRRAIYYQKLTLQPVDHLTISLQMGTNKVAS
ParentalQKGMSVYGLGRQVYDPKYCAAPTEPVIHN
QK.M.V.GLG.QVY..KYCAA.TE..IHN
RetrocopyQKRMGVHGLGGQVYGRKYCAALTETIIHN

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 281 .77 RPM
bodymap2_adrenal 0 .02 RPM 315 .72 RPM
bodymap2_brain 0 .00 RPM 243 .05 RPM
bodymap2_breast 0 .00 RPM 222 .51 RPM
bodymap2_colon 0 .00 RPM 389 .52 RPM
bodymap2_heart 0 .00 RPM 62 .58 RPM
bodymap2_kidney 0 .00 RPM 435 .36 RPM
bodymap2_liver 0 .00 RPM 119 .47 RPM
bodymap2_lung 0 .00 RPM 1028 .52 RPM
bodymap2_lymph_node 0 .00 RPM 333 .77 RPM
bodymap2_ovary 0 .00 RPM 459 .62 RPM
bodymap2_prostate 0 .00 RPM 239 .90 RPM
bodymap2_skeletal_muscle 0 .00 RPM 28 .81 RPM
bodymap2_testis 0 .00 RPM 253 .03 RPM
bodymap2_thyroid 0 .00 RPM 184 .38 RPM
bodymap2_white_blood_cells 0 .00 RPM 2 .68 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3419 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3419 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3419 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3419 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3419 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2323
Gorilla gorilla retro_ggor_2312
Parental genes homology:
Parental genes homology involve 14 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167071 retrocopy
retro_amel_1412,
Bos taurus ENSBTAG000000203451 retrocopy
retro_btau_1211,
Callithrix jacchus ENSCJAG000000181283 retrocopies
retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Echinops telfairi ENSETEG000000100951 retrocopy
retro_etel_638,
Homo sapiens ENSG0000006466616 retrocopies
retro_hsap_1168, retro_hsap_1575, retro_hsap_1697, retro_hsap_2127, retro_hsap_2495, retro_hsap_255, retro_hsap_2576, retro_hsap_2764, retro_hsap_3505, retro_hsap_4168, retro_hsap_4170, retro_hsap_4175, retro_hsap_4257, retro_hsap_4269, retro_hsap_4326, retro_hsap_943,
Homo sapiens ENSG00000117519 1 retrocopy
retro_hsap_3419 ,
Homo sapiens ENSG000001587101 retrocopy
retro_hsap_4108,
Gorilla gorilla ENSGGOG000000138701 retrocopy
retro_ggor_2312,
Macropus eugenii ENSMEUG000000029212 retrocopies
retro_meug_2020, retro_meug_42,
Macaca mulatta ENSMMUG000000016901 retrocopy
retro_mmul_1747,
Monodelphis domestica ENSMODG000000043261 retrocopy
retro_mdom_442,
Mus musculus ENSMUSG000000539312 retrocopies
retro_mmus_1052, retro_mmus_2544,
Sarcophilus harrisii ENSSHAG000000026701 retrocopy
retro_shar_567,
Vicugna pacos ENSVPAG000000048892 retrocopies
retro_vpac_190, retro_vpac_449,

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 = 0.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 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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