RetrogeneDB ID:

retro_hsap_1881

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:39398926..39399385(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225253
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C15orf40
Ensembl ID:ENSG00000169609
Aliases:None
Description:chromosome 15 open reading frame 40 [Source:HGNC Symbol;Acc:28443]


Retrocopy-Parental alignment summary:






>retro_hsap_1881
ATGCTGGGGCTTGGCAGCGGGCTGAAGCAGCTCAAGGGCAGCACTGAGTACTCAGGACTCCACTCGGCTCCCTCTTGGCA
CCAAGATGCCAAGAAAGCTGATGCAATGACCTAGGGTAAAAGTCAGATCAAGGAACCAGAGAGACCACTTCCTCCCTTAG
GTCCTGTGGCAGTTGTTCCTATAGGTTGTGTCACCATAGCCATCCATGCCAAACCTGGCTCCAAACAAAATACTGTAACA
GATTTGACAGCACAGTTGGTAAATGTGGCTATTGCAGCACCTCCATCAGTGGGGGAGGATAATGCTGAGCTTTGTAGCTT
ATCTGTCCAAGGTCTTAGAACTCAGGAAGAGTGATGTGGTTTTGGATACGGGTGGTACATCGCTGAAAAGGTAGTGAAGC
TTTTGGCCTCCACAACTCCAGAAGAAATCTTGAGGAAATTTAAAAAGAAAGCTGAAAAA

ORF - retro_hsap_1881 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.43 %
Parental protein coverage: 99.35 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMLRLRSGLRHL-RATPNTRGSARL-LCAEMP-KKAGATTKGKSQSKEPERPLPPLGPVAVDPKGCVTIAI
ML.L.SGL..L.RA...T..S.RL.L...MP.KKA.A.T.GKSQ.KEPERPLPPLGPVAV.P.GCVTIAI
RetrocopyMLGLGSGLKQL>RAALSTQDSTRLPLGTKMP<KKADAMT*GKSQIKEPERPLPPLGPVAVVPIGCVTIAI
ParentalHAKPGSKQNAVTDLTAEAVNVAIAAPPSEGEANAELC-RYLSKVLELRKSDVVLDKGGKS-REKVVKLLA
HAKPGSKQN.VTDLTA..VNVAIAAPPS.GE.NAELC..YLSKVLELRKSDVVLD.GG.S..EKVVKLLA
RetrocopyHAKPGSKQNTVTDLTAQLVNVAIAAPPSVGEDNAELC>AYLSKVLELRKSDVVLDTGGTS<AEKVVKLLA
ParentalSTTPEEILEKLKKEAKK
STTPEEIL.K.KK.A.K
RetrocopySTTPEEILRKFKKKAEK

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 7 .45 RPM
bodymap2_adrenal 0 .00 RPM 15 .15 RPM
bodymap2_brain 0 .00 RPM 8 .88 RPM
bodymap2_breast 0 .00 RPM 8 .91 RPM
bodymap2_colon 0 .00 RPM 5 .41 RPM
bodymap2_heart 0 .00 RPM 3 .45 RPM
bodymap2_kidney 0 .00 RPM 10 .84 RPM
bodymap2_liver 0 .00 RPM 4 .75 RPM
bodymap2_lung 0 .00 RPM 5 .47 RPM
bodymap2_lymph_node 0 .00 RPM 8 .15 RPM
bodymap2_ovary 0 .00 RPM 10 .85 RPM
bodymap2_prostate 0 .00 RPM 10 .96 RPM
bodymap2_skeletal_muscle 0 .00 RPM 4 .26 RPM
bodymap2_testis 0 .04 RPM 11 .14 RPM
bodymap2_thyroid 0 .00 RPM 15 .86 RPM
bodymap2_white_blood_cells 0 .00 RPM 7 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1881 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1881 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1881 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1881 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1881 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1378
Pongo abelii retro_pabe_1561
Callithrix jacchus retro_cjac_1108
Parental genes homology:
Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000165222 retrocopies
retro_btau_1724, retro_btau_485,
Canis familiaris ENSCAFG000000131852 retrocopies
retro_cfam_39, retro_cfam_420,
Callithrix jacchus ENSCJAG000000158772 retrocopies
retro_cjac_1108, retro_cjac_4086,
Equus caballus ENSECAG000000224591 retrocopy
retro_ecab_374,
Homo sapiens ENSG00000169609 1 retrocopy
retro_hsap_1881 ,
Gorilla gorilla ENSGGOG000000230621 retrocopy
retro_ggor_1378,
Microcebus murinus ENSMICG000000095642 retrocopies
retro_mmur_1387, retro_mmur_1601,
Myotis lucifugus ENSMLUG000000075151 retrocopy
retro_mluc_2487,
Macaca mulatta ENSMMUG000000158901 retrocopy
retro_mmul_664,
Monodelphis domestica ENSMODG000000193741 retrocopy
retro_mdom_145,
Nomascus leucogenys ENSNLEG000000109301 retrocopy
retro_nleu_1803,
Oryctolagus cuniculus ENSOCUG000000050721 retrocopy
retro_ocun_211,
Procavia capensis ENSPCAG000000164461 retrocopy
retro_pcap_51,
Pongo abelii ENSPPYG000000067371 retrocopy
retro_pabe_1561,
Rattus norvegicus ENSRNOG000000195142 retrocopies
retro_rnor_1547, retro_rnor_2334,
Sorex araneus ENSSARG000000063141 retrocopy
retro_sara_147,
Sarcophilus harrisii ENSSHAG000000179472 retrocopies
retro_shar_233, retro_shar_442,
Sus scrofa ENSSSCG000000301311 retrocopy
retro_sscr_221,
Tupaia belangeri ENSTBEG000000143876 retrocopies
retro_tbel_1151, retro_tbel_2000, retro_tbel_3071, retro_tbel_3546, retro_tbel_4182, retro_tbel_4371,

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 = 0.02 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 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017