RetrogeneDB ID:

retro_hsap_2602

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:1771737..1772158(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000214074
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSG00000198242
Aliases:None
Description:ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]


Retrocopy-Parental alignment summary:






>retro_hsap_2602
CCAGCTCCTAAACCTCCCAAGGCCAAAGCCAAAGGCTTTGAAAGCCAAGAAGGCAGTACTGAAAGGCGTCCACAGCCACA
AATTCAAGAAGATTCACACACCACTCACCTTCTGGGGTCCAAGACACTGAGGCTCTGGAGACAGCCCAAATATCCTCGGA
AGAGCACCCCCGGAAGAAACACCAGCCCTGGAGAAACATTCCCCTGACCACTGAGTTCATGGTGAAGAAGAGAGAAGACA
ACAGCACACTTGTGTTCATTGTGGATGTCAAAACCAACAAACACAGGATCAAACTGGCTGTGAAGTTCTCTGACGTTGAT
GTGGCCAAGGTCAACACCATGATATGTCATGGAGAGAAGACATATGTTCCATTGACTCCTGCTATGAGGCTTTGGATGTT
GCCAACAAAATTGGAATCATC

ORF - retro_hsap_2602 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.55 %
Parental protein coverage: 94.23 %
Number of stop codons detected: 0
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalPAPPKAEAKAK-ALKAKKAVLKGVHSHKKKKIRTSPTFRRP-KTLRLRRQPKYPRKSA-PRRNKLDHYAI
PAP....AKAK.ALKAKKAVLKGVHSHK.KKI.T..TF..P.KTLRL.RQPKYPRKS..PR.....H...
RetrocopyPAPKPPKAKAK>ALKAKKAVLKGVHSHKFKKIHTPLTFWGP<KTLRLWRQPKYPRKST<PRKK---HQPW
ParentalIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPD-YD
...PLTTE...KK.EDN.TLVFIVDVK.NKH.IK.AV.K..D.DVAKVNT.I...GE.K.YV.L.P..Y.
RetrocopyRNIPLTTEFMVKKREDNSTLVFIVDVKTNKHRIKLAV-KFSDVDVAKVNTMI-CHGE-KTYVPLTPA<YE
ParentalALDVANKIGII
ALDVANKIGII
RetrocopyALDVANKIGII

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 192 .56 RPM
bodymap2_adrenal 0 .00 RPM 242 .36 RPM
bodymap2_brain 0 .00 RPM 43 .88 RPM
bodymap2_breast 0 .00 RPM 119 .40 RPM
bodymap2_colon 0 .00 RPM 221 .12 RPM
bodymap2_heart 0 .00 RPM 56 .34 RPM
bodymap2_kidney 0 .00 RPM 85 .35 RPM
bodymap2_liver 0 .00 RPM 67 .28 RPM
bodymap2_lung 0 .00 RPM 194 .32 RPM
bodymap2_lymph_node 0 .00 RPM 239 .11 RPM
bodymap2_ovary 0 .00 RPM 286 .76 RPM
bodymap2_prostate 0 .00 RPM 296 .99 RPM
bodymap2_skeletal_muscle 0 .00 RPM 185 .41 RPM
bodymap2_testis 0 .00 RPM 126 .20 RPM
bodymap2_thyroid 0 .00 RPM 127 .58 RPM
bodymap2_white_blood_cells 0 .00 RPM 333 .55 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2602 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2602 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2602 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2602 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2602 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 15 parental genes, and 274 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000463946 retrocopies
retro_btau_132, retro_btau_159, retro_btau_169, retro_btau_178, retro_btau_237, retro_btau_8,
Callithrix jacchus ENSCJAG000000131267 retrocopies
retro_cjac_118, retro_cjac_154, retro_cjac_20, retro_cjac_258, retro_cjac_30, retro_cjac_315, retro_cjac_46,
Felis catus ENSFCAG0000000402135 retrocopies
retro_fcat_1003, retro_fcat_1011, retro_fcat_1030, retro_fcat_1039, retro_fcat_1054, retro_fcat_1071, retro_fcat_1073, retro_fcat_11, retro_fcat_1124, retro_fcat_1161, retro_fcat_1202, retro_fcat_1205, retro_fcat_1275, retro_fcat_1389, retro_fcat_1659, retro_fcat_1670, retro_fcat_1748, retro_fcat_1787, retro_fcat_1796, retro_fcat_1810, retro_fcat_182, retro_fcat_185, retro_fcat_1856, retro_fcat_1905, retro_fcat_1909, retro_fcat_1944, retro_fcat_2022, retro_fcat_289, retro_fcat_364, retro_fcat_476, retro_fcat_603, retro_fcat_657, retro_fcat_765, retro_fcat_898, retro_fcat_950,
Homo sapiens ENSG00000198242 57 retrocopies
retro_hsap_110, retro_hsap_1139, retro_hsap_1177, retro_hsap_1315, retro_hsap_1316, retro_hsap_1460, retro_hsap_1616, retro_hsap_1660, retro_hsap_1714, retro_hsap_1775, retro_hsap_1791, retro_hsap_1807, retro_hsap_1833, retro_hsap_1924, retro_hsap_1970, retro_hsap_2021, retro_hsap_2024, retro_hsap_2134, retro_hsap_2169, retro_hsap_2210, retro_hsap_2222, retro_hsap_2271, retro_hsap_2310, retro_hsap_2356, retro_hsap_2359, retro_hsap_2390, retro_hsap_2404, retro_hsap_2446, retro_hsap_2509, retro_hsap_2511, retro_hsap_2528, retro_hsap_2567, retro_hsap_2602 , retro_hsap_2629, retro_hsap_2748, retro_hsap_2804, retro_hsap_2874, retro_hsap_3282, retro_hsap_334, retro_hsap_3377, retro_hsap_341, retro_hsap_342, retro_hsap_345, retro_hsap_3545, retro_hsap_3571, retro_hsap_3815, retro_hsap_4118, retro_hsap_4127, retro_hsap_4329, retro_hsap_490, retro_hsap_504, retro_hsap_641, retro_hsap_672, retro_hsap_725, retro_hsap_751, retro_hsap_775, retro_hsap_945,
Gorilla gorilla ENSGGOG0000001673626 retrocopies
retro_ggor_1027, retro_ggor_1028, retro_ggor_1123, retro_ggor_120, retro_ggor_123, retro_ggor_1284, retro_ggor_140, retro_ggor_1431, retro_ggor_158, retro_ggor_1650, retro_ggor_1743, retro_ggor_1789, retro_ggor_1911, retro_ggor_1948, retro_ggor_2164, retro_ggor_2239, retro_ggor_2285, retro_ggor_229, retro_ggor_2409, retro_ggor_2475, retro_ggor_2568, retro_ggor_2764, retro_ggor_2773, retro_ggor_580, retro_ggor_611, retro_ggor_642,
Loxodonta africana ENSLAFG0000001338716 retrocopies
retro_lafr_1176, retro_lafr_153, retro_lafr_237, retro_lafr_33, retro_lafr_335, retro_lafr_442, retro_lafr_510, retro_lafr_525, retro_lafr_551, retro_lafr_557, retro_lafr_643, retro_lafr_78, retro_lafr_891, retro_lafr_908, retro_lafr_957, retro_lafr_96,
Myotis lucifugus ENSMLUG000000124484 retrocopies
retro_mluc_175, retro_mluc_2375, retro_mluc_353, retro_mluc_91,
Monodelphis domestica ENSMODG000000192973 retrocopies
retro_mdom_120, retro_mdom_870, retro_mdom_912,
Mustela putorius furoENSMPUG0000001417912 retrocopies
retro_mputfur_102, retro_mputfur_106, retro_mputfur_123, retro_mputfur_159, retro_mputfur_168, retro_mputfur_179, retro_mputfur_3, retro_mputfur_333, retro_mputfur_42, retro_mputfur_52, retro_mputfur_599, retro_mputfur_91,
Mus musculus ENSMUSG000000585468 retrocopies
retro_mmus_1, retro_mmus_126, retro_mmus_130, retro_mmus_184, retro_mmus_224, retro_mmus_64, retro_mmus_84, retro_mmus_95,
Pongo abelii ENSPPYG0000000810849 retrocopies
retro_pabe_1030, retro_pabe_1203, retro_pabe_1206, retro_pabe_1335, retro_pabe_1430, retro_pabe_1459, retro_pabe_1590, retro_pabe_1721, retro_pabe_1747, retro_pabe_1752, retro_pabe_1766, retro_pabe_1797, retro_pabe_1846, retro_pabe_1848, retro_pabe_1867, retro_pabe_1926, retro_pabe_1947, retro_pabe_1995, retro_pabe_2018, retro_pabe_2057, retro_pabe_2075, retro_pabe_2082, retro_pabe_2091, retro_pabe_2132, retro_pabe_2156, retro_pabe_2221, retro_pabe_2334, retro_pabe_234, retro_pabe_243, retro_pabe_2612, retro_pabe_2738, retro_pabe_2773, retro_pabe_2820, retro_pabe_2944, retro_pabe_3006, retro_pabe_3036, retro_pabe_3200, retro_pabe_3371, retro_pabe_3477, retro_pabe_351, retro_pabe_3528, retro_pabe_354, retro_pabe_474, retro_pabe_627, retro_pabe_754, retro_pabe_765, retro_pabe_799, retro_pabe_946, retro_pabe_984,
Rattus norvegicus ENSRNOG000000233446 retrocopies
retro_rnor_136, retro_rnor_145, retro_rnor_211, retro_rnor_40, retro_rnor_404, retro_rnor_62,
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies
retro_shar_188, retro_shar_373, retro_shar_407, retro_shar_448, retro_shar_498, retro_shar_564, retro_shar_624, retro_shar_630, retro_shar_685, retro_shar_698, retro_shar_824, retro_shar_829, retro_shar_835,
Sus scrofa ENSSSCG000000177689 retrocopies
retro_sscr_1025, retro_sscr_1047, retro_sscr_1133, retro_sscr_239, retro_sscr_356, retro_sscr_418, retro_sscr_598, retro_sscr_638, retro_sscr_952,
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies
retro_itri_1022, retro_itri_1035, retro_itri_1051, retro_itri_1059, retro_itri_1071, retro_itri_1150, retro_itri_1261, retro_itri_1327, retro_itri_1347, retro_itri_1460, retro_itri_1507, retro_itri_217, retro_itri_225, retro_itri_304, retro_itri_360, retro_itri_494, retro_itri_626, retro_itri_627, retro_itri_734, retro_itri_761, retro_itri_791, retro_itri_965, retro_itri_972,

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_2602 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2602 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. 3:1770991..1780590 99.18 98.86 99.48 100 100 100 100 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 3:1770991..1780590.

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 99.18 % Yoruba in Ibadan,Nigeria YRI 98.86 % Luhya in Webuye,Kenya LWK 99.48 % 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 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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