RetrogeneDB ID:

retro_hsap_2654

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:65673454..65674048(+)
Located in intron of:ENSG00000151276
Retrocopy
information
Ensembl ID:ENSG00000244226
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ILF2
Ensembl ID:ENSG00000143621
Aliases:ILF2, NF45, PRO3063
Description:interleukin enhancer binding factor 2 [Source:HGNC Symbol;Acc:6037]


Retrocopy-Parental alignment summary:






>retro_hsap_2654
GACGAAACTGGCTTGGAAATCAGTTCTTCTGATGCTACAGTGAAGACTGTCATTACAACAGTGCCACCCAGTCTTCCAAA
ACTGGACCCAGAACTCCGTTTGGATATCAAGGTATTGCAGGGTGCCTTAGCAGCCATTCGGCATGCCCGCTGGTTCAAGG
AAAATGGCTCTCAGTTCACAGTTAAAGTTATCATCAGACTACTGAAGGACTTGAGGGTTTCGTTTTCCTGGCTTTGAGCC
CCTCACACCCTGGATCCTAGGCCTACTAAGTCATTATGCTGTGATAACCCCAACAGACAGCCTTTGGCCCTGAACACTGC
ACATAGGTGTTGCTTGCAGATTCTAGGTGCAGGACTGTTCCTGCCAGGGTCCATGGGTATCACTGACCCCCGTGAGAGCG
GCAACTTCAGAGTACACACAGTCATGACCCTAGAACAGCAGGACATAGTCTGCTACACAGCCCAGACTCTGGTCTGAATC
CTCTCACATGGTGGCTTTAGGAAGATCCTTGGCCAGGAGGGTGATGCCAGACATCTTACTTCTGAAATATCTACCTGGGA
TGGAGTGATAGTAACACCTTCAGAAAAGGCTTAC

ORF - retro_hsap_2654 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.58 %
Parental protein coverage: 51.03 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSALAAIRHARWFEENASQSTVKVLIRLLKD
.ETG.EISSSDATVK..ITTVPP.L.KLDPEL.LDIKVLQ.ALAAIRHARWF.EN.SQ.TVKV.IRLLKD
RetrocopyDETGLEISSSDATVKTVITTVPPSLPKLDPELRLDIKVLQGALAAIRHARWFKENGSQFTVKVIIRLLKD
ParentalLRI-RFPGFEPLTPWILDLLGHYAVMNNPT-RQPLALNVAYRRCLQILAAGLFLPGSVGITDPCESGNFR
LR..RFPGFEPLTPWIL.LL.HYAV...PT.RQPLALN.A.R.CLQIL.AGLFLPGS.GITDP.ESGNFR
RetrocopyLRV>RFPGFEPLTPWILGLLSHYAVI-TPT<RQPLALNTAHRCCLQILGAGLFLPGSMGITDPRESGNFR
ParentalVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVTPSEKAY
VHTVMTLEQQD.VCYTAQTLV.ILSHGGFRKILGQEGDA..L.SEISTWDGVIVTPSEKAY
RetrocopyVHTVMTLEQQDIVCYTAQTLV*ILSHGGFRKILGQEGDARHLTSEISTWDGVIVTPSEKAY

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 79 .11 RPM
bodymap2_adrenal 0 .06 RPM 92 .89 RPM
bodymap2_brain 0 .00 RPM 66 .57 RPM
bodymap2_breast 0 .04 RPM 73 .17 RPM
bodymap2_colon 0 .00 RPM 59 .57 RPM
bodymap2_heart 0 .04 RPM 50 .23 RPM
bodymap2_kidney 0 .00 RPM 102 .66 RPM
bodymap2_liver 0 .02 RPM 42 .97 RPM
bodymap2_lung 0 .00 RPM 122 .59 RPM
bodymap2_lymph_node 0 .00 RPM 88 .57 RPM
bodymap2_ovary 0 .00 RPM 138 .97 RPM
bodymap2_prostate 0 .09 RPM 67 .95 RPM
bodymap2_skeletal_muscle 0 .00 RPM 70 .11 RPM
bodymap2_testis 0 .00 RPM 161 .08 RPM
bodymap2_thyroid 0 .00 RPM 129 .33 RPM
bodymap2_white_blood_cells 0 .00 RPM 101 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2654 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2654 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2654 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2654 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2654 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1789
Pongo abelii retro_pabe_2318
Parental genes homology:
Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000143621 2 retrocopies
retro_hsap_1405, retro_hsap_2654 ,
Macropus eugenii ENSMEUG000000036511 retrocopy
retro_meug_1174,
Microcebus murinus ENSMICG000000137301 retrocopy
retro_mmur_206,
Myotis lucifugus ENSMLUG000000018473 retrocopies
retro_mluc_1046, retro_mluc_217, retro_mluc_2402,
Oryctolagus cuniculus ENSOCUG000000054301 retrocopy
retro_ocun_1216,
Pongo abelii ENSPPYG000000008001 retrocopy
retro_pabe_2318,
Ictidomys tridecemlineatus ENSSTOG000000006671 retrocopy
retro_itri_130,
Tarsius syrichta ENSTSYG000000120613 retrocopies
retro_tsyr_1448, retro_tsyr_1745, retro_tsyr_496,

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:

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





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