RetrogeneDB ID:

retro_pabe_1586

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:18:23169767..23170410(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4X
Ensembl ID:ENSPPYG00000020462
Aliases:None
Description:ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]


Retrocopy-Parental alignment summary:






>retro_pabe_1586
GGTCCCAAGAAGCATCTGAAGTGGGCAGCAGCTCCATGGCATTTGATGCTGGATAAATTGACCCGTGTGGTTGCTCCTCA
TCGATCCACCCATCCCCATCCCCACAAGCTAAGAGAGTGTCTCTCCCTCATCTTTTCCTAAAGAACAGACTTAAGTATGT
CAGACACAAGATGAAGTAAAGAAGATTTTCATGCACAGTTTCATTAAGATCAATGGCAAGGTCTGAACTAATGTAACATA
CCCTGCTGGATTCATGGCTGTCATGAGCACTGACAAGACGGGAGAGAATTTCCGTCTGATCTATGGCACCAAGGCTCCCT
TTGCTGTACATCGTATTGCACCTGAGGAGGCCAAGTACAAGTTGTGCAAAGTGAGAAAAATATTTGTGGACACAAAAGGA
ATCCCTCATCTGCTGACTCTTGGTGCTCACACCATCTGCTACCCTGATCCCCTCATCAAGGTGAATGACACCATTCAGGC
TGATTTGGAGAATGGCAAGATTACTGGTTTCATCAGGTTCAACACTGGGAACCTGTGTATGGTGACTGGAGGTGCTAACC
TGGGAAGAATTGGTGCAATCACCGACAGAGAGAGGCACCCTGGTTCTTTTGATGTGGTTCATGAGAAAGATGCCAACAGC
AAC

ORF - retro_pabe_1586 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.88 %
Parental protein coverage: 80.99 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPH--KLRECLPLI-IFLRNRLKYAL-TGDEVKKICMQRF
GPKKHLK..AAP.H.MLDKLT.V.AP..ST.PH..KLRECL.LI..FL.NRLKY...T.DEVKKI.M..F
RetrocopyGPKKHLKWAAAPWHLMLDKLTRVVAPHRSTHPHPHKLRECLSLI<LFLKNRLKYVR<TQDEVKKIFMHSF
ParentalIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
IKI.GKV.T..TYPAGFM.V.S.DKTGENFRLIY.TK..FAVHRI.PEEAKYKLCKVRKIFV.TKGIPHL
RetrocopyIKINGKV*TNVTYPAGFMAVMSTDKTGENFRLIYGTKAPFAVHRIAPEEAKYKLCKVRKIFVDTKGIPHL
ParentalVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVH
.T..A.TI.YPDPLIKVNDTIQ.DLE.GKIT.FI.F.TGNLCMVTGGANLGRIG.IT.RERHPGSFDVVH
RetrocopyLTLGAHTICYPDPLIKVNDTIQADLENGKITGFIRFNTGNLCMVTGGANLGRIGAITDRERHPGSFDVVH
ParentalVKDANGN
.KDAN.N
RetrocopyEKDANSN

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
SRP007412_brain_prefrontal_cortex 0 .06 RPM 58 .39 RPM
SRP007412_cerebellum 0 .00 RPM 73 .08 RPM
SRP007412_heart 0 .03 RPM 87 .60 RPM
SRP007412_kidney 0 .03 RPM 131 .16 RPM
SRP007412_liver 0 .00 RPM 137 .65 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1586 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1586 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1586 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1868
Pan troglodytes retro_ptro_1280
Gorilla gorilla retro_ggor_1367
Parental genes homology:
Parental genes homology involve 26 parental genes, and 246 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
Bos taurus ENSBTAG000000188005 retrocopies
retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris ENSCAFG000000171512 retrocopies
retro_cfam_165, retro_cfam_194,
Callithrix jacchus ENSCJAG000000041922 retrocopies
retro_cjac_19, retro_cjac_361,
Cavia porcellus ENSCPOG000000063373 retrocopies
retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus ENSECAG000000108526 retrocopies
retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens ENSG000001298241 retrocopy
retro_hsap_1704,
Homo sapiens ENSG0000019803419 retrocopies
retro_hsap_1070, retro_hsap_1151, retro_hsap_120, retro_hsap_1204, retro_hsap_1792, retro_hsap_1868, retro_hsap_2026, retro_hsap_2051, retro_hsap_2052, retro_hsap_2270, retro_hsap_2437, retro_hsap_2443, retro_hsap_3162, retro_hsap_3423, retro_hsap_3519, retro_hsap_3986, retro_hsap_4051, retro_hsap_656, retro_hsap_875,
Loxodonta africana ENSLAFG000000026544 retrocopies
retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii ENSMEUG0000000796916 retrocopies
retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Microcebus murinus ENSMICG0000001660658 retrocopies
retro_mmur_1107, retro_mmur_1108, retro_mmur_1123, retro_mmur_1136, retro_mmur_1168, retro_mmur_1208, retro_mmur_1209, retro_mmur_1229, retro_mmur_1231, retro_mmur_1257, retro_mmur_1268, retro_mmur_1334, retro_mmur_1411, retro_mmur_1416, retro_mmur_1430, retro_mmur_1442, retro_mmur_1454, retro_mmur_1467, retro_mmur_1471, retro_mmur_1519, retro_mmur_1578, retro_mmur_1584, retro_mmur_1599, retro_mmur_1600, retro_mmur_1611, retro_mmur_166, retro_mmur_241, retro_mmur_281, retro_mmur_289, retro_mmur_293, retro_mmur_347, retro_mmur_363, retro_mmur_390, retro_mmur_510, retro_mmur_511, retro_mmur_521, retro_mmur_523, retro_mmur_530, retro_mmur_54, retro_mmur_551, retro_mmur_591, retro_mmur_609, retro_mmur_619, retro_mmur_663, retro_mmur_665, retro_mmur_687, retro_mmur_767, retro_mmur_784, retro_mmur_828, retro_mmur_840, retro_mmur_917, retro_mmur_918, retro_mmur_931, retro_mmur_943, retro_mmur_946, retro_mmur_949, retro_mmur_96, retro_mmur_995,
Monodelphis domestica ENSMODG000000110701 retrocopy
retro_mdom_238,
Mustela putorius furoENSMPUG0000000529411 retrocopies
retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus ENSMUSG0000003132013 retrocopies
retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Nomascus leucogenys ENSNLEG0000001812125 retrocopies
retro_nleu_1127, retro_nleu_1226, retro_nleu_1361, retro_nleu_142, retro_nleu_1442, retro_nleu_1907, retro_nleu_1908, retro_nleu_2089, retro_nleu_2256, retro_nleu_244, retro_nleu_2461, retro_nleu_2495, retro_nleu_2587, retro_nleu_2613, retro_nleu_2640, retro_nleu_2646, retro_nleu_2776, retro_nleu_2801, retro_nleu_2932, retro_nleu_2967, retro_nleu_2968, retro_nleu_486, retro_nleu_500, retro_nleu_560, retro_nleu_947,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Procavia capensis ENSPCAG000000007613 retrocopies
retro_pcap_334, retro_pcap_35, retro_pcap_360,
Pongo abelii ENSPPYG00000020462 24 retrocopies
retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586 , retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes ENSPTRG000000220259 retrocopies
retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,