RetrogeneDB ID:

retro_hsap_2569

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:17997379..17998114(-)
Located in intron of:ENSG00000099954
Retrocopy
information
Ensembl ID:ENSG00000228045
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJA1
Ensembl ID:ENSG00000086061
Aliases:DNAJA1, DJ-2, DjA1, HDJ2, HSDJ, HSJ2, HSPF4, NEDD7, hDJ-2
Description:DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]


Retrocopy-Parental alignment summary:






>retro_hsap_2569
AAAATGGCTTTGAAGTAATACCCTGGTAAGAATCTAAATGAAGGAGAGAAGTTAAATGGATTTCTCAATCTTGAGAAGTT
CTCTCTGATGCAGAGAATAGGGAATTCTATGACAAAGGAGGACAGGCAATTAAAGAGGGTGGGGCTGGTGGCAGTTCTCA
TTCCCCCATGGACATCTCTGCTAAGTTTTTTTGGGGGAGAAGGAAGGATACTAAGAGAAAGGAGAGGTAAAAACTCCTAC
ATCAGCTCTCAGTAGCCTTAGGAGATCTATCCAATGGTGAAAAAAGAAAACTGGCTCTGCAAAAGAATATGATTTGTGAC
AAATGTGAAGGCAGAGGTGTTAAGAAGGGAGCAGGATCCTGCTGTGCCAACTGCTGAGGTGCTTGAATGCAAACAGTAAT
TCATCAATAAGACCTGGAATGGTTCAGCAAATTCAATCTGTGTGCATGGAGTGCCAAGCCCATGGGGAAACCATCCGTCC
TAAAGATAGACGTGAAAGCTGCAATGGAAGGAAGACAGTTGCAGAGAAGGAGATTCTAGAAGTCCCTATTGACAAAGGCA
TGAAAGATGGCCAGAAGATAACATTCCGTGGTGAAGGATACCAAGACCAGAACTGGAGCCAGGAAACATTACCACTGGGG
TAGAACAGAAAGACCATGCTATTTTTACTTGACAGGGAGAAGACCTTTTCCTGTGTACAGACACACAGCTGGCTGAAACA
CTGTGTGACTCCCAA

ORF - retro_hsap_2569 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.63 %
Parental protein coverage: 62.22 %
Number of stop codons detected: 5
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalKLALKYHPDKNPNEGEKF-KQISQAYEVLSDAKKRELYDKGGEQAIKEGGAGGGFGSPMDI-FDMFFGGG
K.ALK..P.KN.NEGEK..K.ISQ..EVLSDA..RE.YDKGG.QAIKEGGAGG...SPMDI....FFGG.
RetrocopyKMALK*YPGKNLNEGEKL<KWISQS*EVLSDAENREFYDKGG-QAIKEGGAGGSSHSPMDI>LLSFFGGE
ParentalGRMQRERRGKN-VVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAVECCPNCRGTGMQIRIHQ
GR..RERRGKN...HQLSV.L.DL.NG..RKLALQKN.ICDKCEGRG.KKGA..CC.NC.G..MQ..IHQ
RetrocopyGRILRERRGKN<LLHQLSVALGDLSNGEKRKLALQKNMICDKCEGRGVKKGAGSCCANC*GA*MQTVIHQ
Parental-IGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQE-P
.I.PGMVQQIQSVCMECQ.HGE.I.PKDR..SCNGRK.V.EK.ILEV.IDKGMKDGQKITF.GEG.Q..P
Retrocopy<IRPGMVQQIQSVCMECQAHGETIRPKDRRESCNGRKTVAEKEILEVPIDKGMKDGQKITFRGEGYQD<P
ParentalGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQ
.LEPG.I.....QKDHA.FT..GEDLF.C.D.QL.E.LC..Q
RetrocopyELEPGNITTGVEQKDHAIFT*QGEDLFLCTDTQLAETLCDSQ

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 97 .58 RPM
bodymap2_adrenal 0 .04 RPM 98 .40 RPM
bodymap2_brain 0 .00 RPM 226 .71 RPM
bodymap2_breast 0 .00 RPM 120 .27 RPM
bodymap2_colon 0 .00 RPM 362 .12 RPM
bodymap2_heart 0 .00 RPM 59 .87 RPM
bodymap2_kidney 0 .00 RPM 242 .40 RPM
bodymap2_liver 0 .00 RPM 88 .80 RPM
bodymap2_lung 0 .00 RPM 282 .31 RPM
bodymap2_lymph_node 0 .00 RPM 340 .47 RPM
bodymap2_ovary 0 .00 RPM 256 .31 RPM
bodymap2_prostate 0 .00 RPM 151 .59 RPM
bodymap2_skeletal_muscle 0 .00 RPM 41 .41 RPM
bodymap2_testis 0 .06 RPM 395 .05 RPM
bodymap2_thyroid 0 .00 RPM 280 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 197 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2569 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2569 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2569 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2569 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2569 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1499
Gorilla gorilla retro_ggor_1603
Pongo abelii retro_pabe_1892
Parental genes homology:
Parental genes homology involve 21 parental genes, and 128 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075894 retrocopies
retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus ENSBTAG000000162656 retrocopies
retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris ENSCAFG0000000181823 retrocopies
retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Callithrix jacchus ENSCJAG0000000802210 retrocopies
retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus ENSCPOG000000004626 retrocopies
retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Dasypus novemcinctus ENSDNOG000000183423 retrocopies
retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Felis catus ENSFCAG000000087295 retrocopies
retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Homo sapiens ENSG00000086061 4 retrocopies
retro_hsap_2331, retro_hsap_2569 , retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla ENSGGOG000000070303 retrocopies
retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus ENSMLUG000000160867 retrocopies
retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica ENSMODG000000033847 retrocopies
retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mustela putorius furoENSMPUG000000042312 retrocopies
retro_mputfur_1543, retro_mputfur_487,
Nomascus leucogenys ENSNLEG000000052684 retrocopies
retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus ENSOCUG000000048332 retrocopies
retro_ocun_516, retro_ocun_70,
Pongo abelii ENSPPYG000000191414 retrocopies
retro_pabe_1892, retro_pabe_2111, retro_pabe_2559, retro_pabe_2994,
Pan troglodytes ENSPTRG000000208524 retrocopies
retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Rattus norvegicus ENSRNOG000000070292 retrocopies
retro_rnor_2208, retro_rnor_608,
Sarcophilus harrisii ENSSHAG000000123661 retrocopy
retro_shar_762,
Ictidomys tridecemlineatus ENSSTOG000000052004 retrocopies
retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tupaia belangeri ENSTBEG0000000059623 retrocopies
retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tursiops truncatus ENSTTRG000000073874 retrocopies
retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,

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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