RetrogeneDB ID:

retro_hsap_2121

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:84258564..84259244(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228225
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CRLF3
Ensembl ID:ENSG00000176390
Aliases:CRLF3, CREME-9, CREME9, CRLM9, CYTOR4, FRWS, p48.2
Description:cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]


Retrocopy-Parental alignment summary:






>retro_hsap_2121
AGTCTCTTGCAAGAGCTGGGCACCATTAAACAGGGGACTATTAAGCCACTAGGTGACTGTCAGGAGTCATACAGCATGAA
ATTAACACCGCAGAGGACTTAATCCAAGAAAGTGAGATCACCATTGTTGGTGGCATGGGAGAACAGATTGAGAAACTGTG
AACCGTTACCAAAAAGGCCTTCTGCATTTAGTTAGACAGGTTACCAGAAGTGTCTCTGCTGGTTGATGTGCCTTGTTTGT
TTGCTCAGCTGAATGACTCAATTCTTATTTTAGTGAAAGGCTACATCTTTCACCATGGAATGGTGGCATCTCACCTACCA
GTAGAAATGTAAGCACTAATAGAGAAAACTGGAAGCCTCATTGTATGATGATGTAAGATAGATGATGACACTATAGCTCA
AGATTACAGATTCCAGCTCCATAAATGTACTTCAAATCATTTTAAGTATGTATGTGTAGGCTCTGAAACTGAATTTATAG
CATTGCACATAGATCCCAATGTTGATTATCAGTTCAGAGTCTATGCCGGAGGGCAGAGGACCAGCTAACAGGAGTGGAGA
CCTTGGAGCATCCTCCAGATATGTTATTCCGTATTGATGCCTCCTGAGTGGACAGCTGGCCTTAAGGGGTATACTCTGAG
CAACTGAAGAAATATATCACTCCAGCTTGATTCTGAATCC

ORF - retro_hsap_2121 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.47 %
Parental protein coverage: 50.9 %
Number of stop codons detected: 7
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTLLQEVDTIEQETIKPLDDCQK-LIEHGVNTAEDLVREGEIAMLGGVGEENEKLWSFTKKASHIQLDSLP
.LLQE..TI.Q.TIKPL.DCQ...I.H..NTAEDL..E.EI...GG.GE..EKL...TKKA..I.LD.LP
RetrocopySLLQELGTIKQGTIKPLGDCQE<VIQHEINTAEDLIQESEITIVGGMGEQIEKL*TVTKKAFCI*LDRLP
ParentalEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGTVASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQ
EV.LLVDVPCL.AQL.DSIL..VK..IF.HG.VAS..PV....LIEK.G..IV..CK.DDD..AQDYR.Q
RetrocopyEVSLLVDVPCLFAQLNDSILILVKGYIFHHGMVASHLPVEM*ALIEKTGSLIV**CKIDDDTIAQDYRFQ
ParentalFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCARGDGR--QEWSPWSVPQIGHSTLVPHEWTAGFE
..KCTSNHF..V.VGSETEFI.LHIDPNVDYQFRV.A.G.....QEW.PWS..QI..S.L.P.EWTAG..
RetrocopyLHKCTSNHFKYVCVGSETEFIALHIDPNVDYQFRVYAGGQRTS*QEWRPWSILQICYSVLMPPEWTAGLK
ParentalGYSLSSRRNIALRNDSES
GY.LS..RNI.L..DSES
RetrocopyGYTLSN*RNISLQLDSES

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 17 .63 RPM
bodymap2_adrenal 0 .00 RPM 44 .73 RPM
bodymap2_brain 0 .02 RPM 11 .98 RPM
bodymap2_breast 0 .00 RPM 13 .97 RPM
bodymap2_colon 0 .00 RPM 13 .05 RPM
bodymap2_heart 0 .00 RPM 7 .00 RPM
bodymap2_kidney 0 .00 RPM 14 .46 RPM
bodymap2_liver 0 .00 RPM 5 .68 RPM
bodymap2_lung 0 .00 RPM 18 .86 RPM
bodymap2_lymph_node 0 .00 RPM 58 .13 RPM
bodymap2_ovary 0 .00 RPM 23 .04 RPM
bodymap2_prostate 0 .00 RPM 16 .82 RPM
bodymap2_skeletal_muscle 0 .00 RPM 4 .91 RPM
bodymap2_testis 0 .00 RPM 33 .82 RPM
bodymap2_thyroid 0 .00 RPM 9 .08 RPM
bodymap2_white_blood_cells 0 .00 RPM 185 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2121 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2121 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2121 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2121 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2121 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1644
Pongo abelii retro_pabe_1984
Macaca mulatta retro_mmul_998
Parental genes homology:
Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000141631 retrocopy
retro_cjac_1183,
Homo sapiens ENSG00000176390 3 retrocopies
retro_hsap_2121 , retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla ENSGGOG000000050023 retrocopies
retro_ggor_1644, retro_ggor_1649, retro_ggor_2278,
Macaca mulatta ENSMMUG000000090692 retrocopies
retro_mmul_1002, retro_mmul_998,
Mus musculus ENSMUSG000000175611 retrocopy
retro_mmus_368,
Nomascus leucogenys ENSNLEG000000058504 retrocopies
retro_nleu_1957, retro_nleu_2534, retro_nleu_2899, retro_nleu_2900,
Pongo abelii ENSPPYG000000081423 retrocopies
retro_pabe_1925, retro_pabe_1984, retro_pabe_2672,
Pan troglodytes ENSPTRG000000089632 retrocopies
retro_ptro_1560, retro_ptro_2175,

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 ) 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 .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:

The presence of retro_hsap_2121 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2121 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 2:84215894..84261700 100 100 100 100 100 100 100 100 100 100 100 100 99.48 100

Indel #1, located at the genomic coordinates 2:84215894..84261700.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 99.48 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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