RetrogeneDB ID:

retro_hsap_2262

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:58688080..58689123(-)
Located in intron of:ENSG00000233723
Retrocopy
information
Ensembl ID:ENSG00000231043
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IK
Ensembl ID:ENSG00000113141
Aliases:IK, CSA2, RED
Description:IK cytokine, down-regulator of HLA II [Source:HGNC Symbol;Acc:5958]


Retrocopy-Parental alignment summary:






>retro_hsap_2262
ATGCCGGAGCGAGATAGTGAGCCGTTCTCCAACCCTTTGGCCCCTGATGGCCACGATGTGGATGATCCTCACTCCTTCCA
CCAATCAAAACTCACCAATGAAGACTTCAGGAAACTTCTCATGACCCCCAGGGCTGCACCTACCTCTGCACCACCTTCTA
AGTCACGTCACCATGAGATGCCAAGGGAGTACAATGAGGATGAAGACCCAGCTGCACGAAGGAGGAAAAAGAAAAGTTAT
TATGCTAAGCTACGCCAACAAGAAATTGAGAGAGAGAGAGAGCTAGCAGAGAAGTACCGGGGTCGTGCCAAGGAACGGAG
AGATGGAGTGAACAAAGATTATGAAGAAACCGAGCTTATCAACACCACAGCTAACTACAGGGCTGTTGGCCCCACTACTA
AGGCGGACAAATCAGCTGCAGAGAAGAGAAGACAGTTGATCCAGGAGTCCAAATTCTTGGGTGGTGACATGGAACACACC
CATTTGGTGAAAGGCTTGGATTTTGCTCTGCTTCAAAAGGTACGAGCTGAGATTGCCAGCAAAGAGAAAGAGGAAGAGGA
ACTGATGGAAAAGCCCCAGAAAGAAACCAAGAAAGATGAGGATCCTGAAAATAAAATTGAATTTAAAACACGTCTGGGCC
GCAATGTTTACCGAGTGCTTTTTAAGAACAAGCATATAAGCGGAATGAGTTGTTCCTGCCGGGCCGCATGGCCTATGTGG
TAGGCCTGGATGATGAGTAAGCTGACACAGATATCCCCACCACTCTTATCCGCAGCAAGGTTGACTGCCCCACCATGGAG
GCCCAGACCATACTGACCACAAATGATATTGTCATTAGCAAGCTTACCCAGTTGCTTTCATACCTGAGGCAGGGAACCCG
TAACAAGAAGCTTAAGAAGAAGGATAAAGGGAAGCTGGAAGAGAAGAAACCTGCTGAGGCTGACAGGAGTATTTTCGAAG
ACATTGGGGATTATACACCCTCCACAATCAAGACACCTTGGGACAAGGAGCGGGAGAGATATCGGGAACGGGAGCGTGAT
CAG

ORF - retro_hsap_2262 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.84 %
Parental protein coverage: 62.48 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPERDSEPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP
MPERDSEPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP
RetrocopyMPERDSEPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP
ParentalAARRRKKKSYYAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADKSAA
AARRRKKKSYYAKLRQQEI.....LAEKYR.RAKERRDGVNKDYEETELI.TTANYRAVGPT..ADKSAA
RetrocopyAARRRKKKSYYAKLRQQEIXXXXXLAEKYRGRAKERRDGVNKDYEETELINTTANYRAVGPTTKADKSAA
ParentalEKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKT
EKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKT
RetrocopyEKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKT
ParentalRLGRNVYRMLFKSK-AYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTNDIVI
RLGRNVYR.LFK.K.AY.RNELFLPGRMAYVV.LDDE.ADTDIPTTLIRSK.DCPTMEAQT.LTTNDIVI
RetrocopyRLGRNVYRVLFKNK<AYKRNELFLPGRMAYVVGLDDE*ADTDIPTTLIRSKVDCPTMEAQTILTTNDIVI
ParentalSKLTQILSYLRQGTRNKKLKKKDKGKLEEKKPPEADMNIFEDIGDYVPSTTKTPRDKERERYRERERDR
SKLTQ.LSYLRQGTRNKKLKKKDKGKLEEKKP.EAD..IFEDIGDY.PST.KTP.DKERERYRERERD.
RetrocopySKLTQLLSYLRQGTRNKKLKKKDKGKLEEKKPAEADRSIFEDIGDYTPSTIKTPWDKERERYRERERDQ

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 134 .32 RPM
bodymap2_adrenal 0 .00 RPM 122 .51 RPM
bodymap2_brain 0 .07 RPM 108 .04 RPM
bodymap2_breast 0 .04 RPM 113 .68 RPM
bodymap2_colon 0 .02 RPM 143 .24 RPM
bodymap2_heart 0 .02 RPM 48 .15 RPM
bodymap2_kidney 0 .00 RPM 74 .14 RPM
bodymap2_liver 0 .00 RPM 31 .79 RPM
bodymap2_lung 0 .02 RPM 99 .75 RPM
bodymap2_lymph_node 0 .02 RPM 86 .96 RPM
bodymap2_ovary 0 .04 RPM 150 .61 RPM
bodymap2_prostate 0 .10 RPM 117 .22 RPM
bodymap2_skeletal_muscle 0 .25 RPM 126 .91 RPM
bodymap2_testis 0 .41 RPM 222 .67 RPM
bodymap2_thyroid 0 .09 RPM 184 .15 RPM
bodymap2_white_blood_cells 0 .08 RPM 135 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2262 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2262 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1239341190 libraries593 libraries46 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_2262 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2262 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2262 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1685
Pongo abelii retro_pabe_1954
Parental genes homology:
Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000097273 retrocopies
retro_dnov_618, retro_dnov_714, retro_dnov_960,
Dipodomys ordii ENSDORG000000065844 retrocopies
retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens ENSG00000113141 1 retrocopy
retro_hsap_2262 ,
Gorilla gorilla ENSGGOG000000133741 retrocopy
retro_ggor_1685,
Loxodonta africana ENSLAFG000000081521 retrocopy
retro_lafr_362,
Otolemur garnettii ENSOGAG000000142811 retrocopy
retro_ogar_1402,
Pongo abelii ENSPPYG000000158611 retrocopy
retro_pabe_1954,
Sorex araneus ENSSARG000000073883 retrocopies
retro_sara_416, retro_sara_419, retro_sara_558,

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 = 0.41 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .15 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .29 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .25 RPM
CEU_NA12751 0 .17 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .19 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .25 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .25 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .19 RPM
FIN_HG00338 0 .21 RPM
FIN_HG00349 0 .23 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .20 RPM
FIN_HG00378 0 .11 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .24 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .17 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .25 RPM
GBR_HG00142 0 .11 RPM
GBR_HG00143 0 .16 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .17 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .29 RPM
TSI_NA20765 0 .15 RPM
TSI_NA20771 0 .31 RPM
TSI_NA20786 0 .16 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .41 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .10 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .13 RPM
YRI_NA19118 0 .15 RPM
YRI_NA19213 0 .19 RPM
YRI_NA19214 0 .25 RPM
YRI_NA19223 0 .26 RPM

Indel association:

The presence of retro_hsap_2262 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2262 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. 2:58688881..58691300 100 100 100 100 100 100 100 100 100 100 100 100 100 99.5

Indel #1, located at the genomic coordinates 2:58688881..58691300.

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 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 99.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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