RetrogeneDB ID:

retro_hsap_480

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:178715820..178716818(-)
Located in intron of:ENSG00000116191
Retrocopy
information
Ensembl ID:ENSG00000228196
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTPN2
Ensembl ID:ENSG00000175354
Aliases:PTPN2, PTN2, PTPT, TC-PTP, TCELLPTP, TCPTP
Description:protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]


Retrocopy-Parental alignment summary:






>retro_hsap_480
GATCACAGTTGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCTTAGTTGACATAGAAGAGGACAAAGG
AGTTACATCTTAACACAGGGTCCACTTCCTAACACATGCTGCCATTTCTGGCTTATGGTTTGGCAGCAGAAGACCAAAGC
AGTTGTCATGCTGAACCGCATTATGGAGAAAGAATTGGTTAAATGTGCACAGTACTGGCCAACAGATGACCAAGAGATGC
TGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTGTCAGAAGATGTGAAGTCGTATTATACAGTACATCTACCACAATTA
GAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTTCATTATACTACTTGGCCAGATTTTGGAGTCCCTCAATC
ACCAGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGACCATGGACCTGTGGTGATCC
ACCGTAGTGCAGGCACTGGACGCTCCAGCACCTTCTCTCTGGTAGACACTTGTCTTGTTTTGATGGAAAAAGGAGATGAT
ATTAACATTAAACAAGTGTTACTGAACATAAGAAAATTCCAAATGGGTCTTATCTCAGACCCCAGATCAACTGAGATTCT
CATACATGGCTATAACAGAAGGAGCAAAATGTGTAAAGGGAGATTCTAGTATACAGAAACGATGGAAAGAACTTTCTAAG
GAAGACTACCTCCTGCTTTTGATCATTCACCAAACAAAATAATGACTGAAAAATACAATAGGAACAGAATAGGTCTAGAA
GAAGAAAAACTGACAGGTGACTGACGTACAGGACTTTCCTCTAAAATGCAAGATACAATGGAGGAGAACAATGAGAGTGT
TCTACGGAAACGTATGTGAGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAATAGAGGCTAAATGAGA
ATGAACGAAAAAGAAAAAGGCCAAGATTGACAGATACC

ORF - retro_hsap_480 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.96 %
Parental protein coverage: 86.05 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalDHSRVKLQNAENDYINASLVDIEE-AQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKC
DHS.VKLQNAENDYINASLVDIEE..QRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRI.EKE.VKC
RetrocopyDHSCVKLQNAENDYINASLVDIEE<GQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIMEKELVKC
ParentalAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFL
AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHL.QLENINSGETRTISHFHYTTWPDFGVP.SPASFL
RetrocopyAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLPQLENINSGETRTISHFHYTTWPDFGVPQSPASFL
ParentalNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLI-QTP
NFLFKVRESGSLNPDHGP.VIH.SAG.GRS.TFSLVDTCLVLMEKGDDINIKQVLLN.RK..MGLI.QTP
RetrocopyNFLFKVRESGSLNPDHGPVVIHRSAGTGRSSTFSLVDTCLVLMEKGDDINIKQVLLNIRKFQMGLI>QTP
ParentalDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKED-LSPAFDHSPNKIMTEKYNGNRIGLEEEKLTGDRCT
DQLRFSYMAI.EGAKC.KGDSSIQKRWKELSKED.L.PAFDHSPNKIMTEKYN.NRIGLEEEKLTGD..T
RetrocopyDQLRFSYMAITEGAKCVKGDSSIQKRWKELSKED<LPPAFDHSPNKIMTEKYNRNRIGLEEEKLTGD*RT
ParentalGLSSKMQDTMEENSESALRKRIREDRKATTAQKVQQMKQRLNENERKRKRPRLTDT
GLSSKMQDTMEEN.ES.LRKR..EDRKATTAQKVQQMK.RLNENERKRKRPRLTDT
RetrocopyGLSSKMQDTMEENNESVLRKRM*EDRKATTAQKVQQMK*RLNENERKRKRPRLTDT

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 22 .36 RPM
bodymap2_adrenal 0 .31 RPM 53 .96 RPM
bodymap2_brain 0 .02 RPM 16 .55 RPM
bodymap2_breast 0 .00 RPM 23 .35 RPM
bodymap2_colon 0 .00 RPM 23 .03 RPM
bodymap2_heart 0 .00 RPM 10 .91 RPM
bodymap2_kidney 0 .08 RPM 24 .47 RPM
bodymap2_liver 0 .08 RPM 12 .53 RPM
bodymap2_lung 0 .00 RPM 43 .25 RPM
bodymap2_lymph_node 0 .00 RPM 54 .88 RPM
bodymap2_ovary 0 .10 RPM 48 .85 RPM
bodymap2_prostate 0 .00 RPM 28 .87 RPM
bodymap2_skeletal_muscle 0 .02 RPM 12 .09 RPM
bodymap2_testis 0 .00 RPM 35 .31 RPM
bodymap2_thyroid 0 .15 RPM 26 .36 RPM
bodymap2_white_blood_cells 0 .00 RPM 55 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_480 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_480 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_480 retrocopy 5' end.

Lab - click to see more details

retro_hsap_480 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_480 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 15 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000008671 retrocopy
retro_chof_2231,
Callithrix jacchus ENSCJAG000000051021 retrocopy
retro_cjac_1577,
Dasypus novemcinctus ENSDNOG000000165881 retrocopy
retro_dnov_1466,
Erinaceus europaeus ENSEEUG000000056361 retrocopy
retro_eeur_370,
Echinops telfairi ENSETEG000000055772 retrocopies
retro_etel_1743, retro_etel_1942,
Homo sapiens ENSG00000175354 2 retrocopies
retro_hsap_1186, retro_hsap_480 ,
Homo sapiens ENSG000001792955 retrocopies
retro_hsap_2823, retro_hsap_3061, retro_hsap_3302, retro_hsap_3670, retro_hsap_4062,
Gorilla gorilla ENSGGOG000000102592 retrocopies
retro_ggor_453, retro_ggor_925,
Loxodonta africana ENSLAFG000000118181 retrocopy
retro_lafr_701,
Macropus eugenii ENSMEUG000000051561 retrocopy
retro_meug_653,
Monodelphis domestica ENSMODG000000214221 retrocopy
retro_mdom_1225,
Nomascus leucogenys ENSNLEG000000090743 retrocopies
retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii ENSOGAG000000286051 retrocopy
retro_ogar_3429,
Pongo abelii ENSPPYG000000089833 retrocopies
retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes ENSPTRG000000098842 retrocopies
retro_ptro_361, retro_ptro_813,

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 = 0.24 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 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 .08 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .12 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .24 RPM

Indel association:

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



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