RetrogeneDB ID:

retro_ptro_2873

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:9:7542650..7543481(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000039806
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL4
Ensembl ID:ENSPTRG00000007195
Aliases:None
Description:ribosomal protein L4 [Source:HGNC Symbol;Acc:10353]


Retrocopy-Parental alignment summary:






>retro_ptro_2873
ATGGCGTGTGCTCGCCCACTGATATCAGTGTGCTCCGAAAAGGGGGAGTCACCTGGCAAAAATGTCACTTTGCCTGCTGT
ATTCAAGGCTCCTATTCGACCAGATATCGTGAACTTTGTTCACACCAACTTGCGCAAAAACAACAGACAGCCCTACGCTG
TCAGTGAATTAGCAGGTCATCAGACCAGCACTGAGTCTTGGGGTACTGGCAGAGCTGTGGCTCGAACTCCCAGAGTTCGA
GGTGGTGGGACTCACCGCTCTGGCCAGGGTGCTTTTGGAAACATGTGTCGCGGAAGCCGAATGTTTGCACCAACCAAAAC
CTGGCGCCGTTGGCATCGTAGAGTGAACACAACCCAAAAACGGTGTGCCATCTGTTCTTCCCTGGCTGCCTCAGCCCTAC
CAGCACTGGTCATGTCTACAGGTCATCGTATTGAGGAAGTTCCTGAACTTCCTTTGGTAGTCGAAGATAAAGTTGAAGGC
TACAGGAAGACCAAGGAAGCTGTTCTGCTCCTTAAGAAACTTAAAGCCCGGAATGATATCAAAAAGGTCTATGCCTCTCA
GCGAATGAGAGCTGGCAAAGGCAAAATGAGAAACCGTCGCCGTATCCAGCGCAGGGGCCCGCGCATCATCTGTAATGAGG
ATAATGGTATCAAGGCCTTCAGAAACATCCCTGCAATTACTCTGCTTAATGTAAGCAAGCTGAACATTTCGAAGCTTGCT
CCTGGTGGGCACGTGGGACGTTTCTGCATTTGGCCTGGAAGTGCTTTCCGGAAGTTAGATGAATTGTATGGCACTTGGCG
TAAAGCCGCTTCCCTCAAGAGTGACTACAAT

ORF - retro_ptro_2873 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.17 %
Parental protein coverage: 82.49 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTG
MACARPLISV.SEKGES.GKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTS.ESWGTG
RetrocopyMACARPLISVCSEKGESPGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSTESWGTG
ParentalRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSK
RAVAR.PRVRGGGTHRSGQGAFGNMCRG.RMFAPTKTWRRWHRRVNTTQKR.AICS.LAASALPALVMS.
RetrocopyRAVARTPRVRGGGTHRSGQGAFGNMCRGSRMFAPTKTWRRWHRRVNTTQKRCAICSSLAASALPALVMST
ParentalGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCII
GHRIEEVPELPLVVEDKVEGY.KTKEAVLLLKKLKA.NDIKKVYASQRMRAGKGKMRNRRRIQRRGP.II
RetrocopyGHRIEEVPELPLVVEDKVEGYRKTKEAVLLLKKLKARNDIKKVYASQRMRAGKGKMRNRRRIQRRGPRII
ParentalYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYH
.NEDNG.IKAFRNIP.ITLLNVSKLNI.KLAPGGHVGRFCIW..SAFRKLDELYGTWRKAASLKS.Y.
RetrocopyCNEDNG-IKAFRNIPAITLLNVSKLNISKLAPGGHVGRFCIWPGSAFRKLDELYGTWRKAASLKSDYN

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 5 .84 RPM 168 .97 RPM
SRP007412_cerebellum 3 .44 RPM 289 .01 RPM
SRP007412_heart 2 .59 RPM 210 .99 RPM
SRP007412_kidney 5 .15 RPM 352 .21 RPM
SRP007412_liver 3 .67 RPM 272 .15 RPM
SRP007412_testis 2 .74 RPM 141 .21 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_2873 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2873 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2873 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4229
Gorilla gorilla retro_ggor_2831
Parental genes homology:
Parental genes homology involve 27 parental genes, and 105 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052112 retrocopies
retro_btau_101, retro_btau_610,
Canis familiaris ENSCAFG000000173091 retrocopy
retro_cfam_72,
Choloepus hoffmanni ENSCHOG000000030086 retrocopies
retro_chof_1014, retro_chof_1496, retro_chof_2219, retro_chof_2616, retro_chof_455, retro_chof_476,
Callithrix jacchus ENSCJAG000000074912 retrocopies
retro_cjac_251, retro_cjac_945,
Dasypus novemcinctus ENSDNOG000000066933 retrocopies
retro_dnov_1028, retro_dnov_1152, retro_dnov_1931,
Equus caballus ENSECAG000000231791 retrocopy
retro_ecab_428,
Echinops telfairi ENSETEG000000003373 retrocopies
retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus ENSFCAG000000122934 retrocopies
retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Homo sapiens ENSG000001744445 retrocopies
retro_hsap_1306, retro_hsap_254, retro_hsap_2898, retro_hsap_4229, retro_hsap_471,
Gorilla gorilla ENSGGOG000000036954 retrocopies
retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Loxodonta africana ENSLAFG000000064943 retrocopies
retro_lafr_1076, retro_lafr_152, retro_lafr_960,
Microcebus murinus ENSMICG000000044196 retrocopies
retro_mmur_1050, retro_mmur_1330, retro_mmur_440, retro_mmur_562, retro_mmur_830, retro_mmur_852,
Myotis lucifugus ENSMLUG000000118092 retrocopies
retro_mluc_121, retro_mluc_198,
Macaca mulatta ENSMMUG000000168442 retrocopies
retro_mmul_2160, retro_mmul_649,
Monodelphis domestica ENSMODG000000096572 retrocopies
retro_mdom_656, retro_mdom_944,
Mustela putorius furoENSMPUG000000003373 retrocopies
retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Nomascus leucogenys ENSNLEG000000129384 retrocopies
retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Pongo abelii ENSPPYG000000065781 retrocopy
retro_pabe_152,
Pan troglodytes ENSPTRG00000007195 6 retrocopies
retro_ptro_1512, retro_ptro_1959, retro_ptro_214, retro_ptro_2873 , retro_ptro_353, retro_ptro_897,
Pteropus vampyrus ENSPVAG0000000006818 retrocopies
retro_pvam_1222, retro_pvam_1342, retro_pvam_201, retro_pvam_202, retro_pvam_216, retro_pvam_236, retro_pvam_267, retro_pvam_399, retro_pvam_428, retro_pvam_430, retro_pvam_435, retro_pvam_466, retro_pvam_518, retro_pvam_736, retro_pvam_778, retro_pvam_819, retro_pvam_865, retro_pvam_955,
Rattus norvegicus ENSRNOG000000093785 retrocopies
retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,
Sus scrofa ENSSSCG000000049452 retrocopies
retro_sscr_138, retro_sscr_885,
Ictidomys tridecemlineatus ENSSTOG000000092211 retrocopy
retro_itri_437,
Tupaia belangeri ENSTBEG000000143929 retrocopies
retro_tbel_1701, retro_tbel_2186, retro_tbel_2649, retro_tbel_3302, retro_tbel_3577, retro_tbel_3624, retro_tbel_3938, retro_tbel_4340, retro_tbel_4402,
Tarsius syrichta ENSTSYG000000055881 retrocopy
retro_tsyr_1144,
Tursiops truncatus ENSTTRG000000102067 retrocopies
retro_ttru_1130, retro_ttru_1399, retro_ttru_1713, retro_ttru_177, retro_ttru_789, retro_ttru_817, retro_ttru_964,
Vicugna pacos ENSVPAG000000067462 retrocopies
retro_vpac_143, retro_vpac_250,


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