RetrogeneDB ID:

retro_ggor_2016

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:4:11196920..11197834(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSGGOG00000025782
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ENSG00000205937
Ensembl ID:ENSGGOG00000014275
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_2016
ATGGATTTATCAGGAGTGAAAAAGAAGAGCTTGCTAGGAGTCAAAGAAAATAATAAAAAGTCCAGCACTAGGGCCCCTTC
ACCTACCAAACGCAAAGACCGCTCAGATGAGAAGTCCAAGGATCGCTCAAAAGATAAAGGGGCCACCAAGGAGTCAAGTG
AGAAGGATCGCGGCCGGGACAAAACGCGAAAGAGGCGCAGCGCTTCCAGTGGTAGCAGCAGTACCAGGTCTCGGTCCAAC
TCGACTTCCAGCTCAGGCTCCAGCACCAGGACTGGCTCAAGCAGTGGCTCCAGCTCTTCCTCAGCATCCAGCCGCTCAGG
AAGCTCCAGCACCTCCCGCAGCTCCAGCTCTAGCAGCTCTTCTGGCTCTCCAAGTCCTTCTCGGCGCAGACACGACAACA
GGAGGCGCTCCCGCTCCAAATCCAAACCACCTAAAAGAGATGAAAAGGAGAGGAAAAGGCGGAGCCCATCTCCTAAGCCC
ACCAAAGTGCACATTGGGAGACTCACCAGGAATGTGACAAAGGATCACGTCATGGAGATATTTTCCACCTATGGGAAAAT
TAAAATGATTGACATGCCCGTGGAAAGGATGCATCCCCATCTGTCCAAAGGCTATGCGTACGTAGAGTTTGAGAATCCAG
ATGAAGCTGAGAAGACGCTGAAGCACATGGATGGAGGACAGATTGATGGCCAGGAGTTCACTGCCACCGCCGTGCTGGCC
CCCTGGCCTAGGCCACCCCCAGGAGATTCAGCCCTCCCAGGAGAATGTTGCCACCGCCGCCTATGTGGTGCAGGTCTCCC
CCACGGATGAGGAGAAGGTCCCGCTCCCCGAGGCGCAGGTCCCCCGTGCGCCGGAGATCACGGTCCCCGGGCCGCCGCCG
CCACAGGAGCCGCTCCAGCTCCAACTCCTCCCGA

ORF - retro_ggor_2016 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.71 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASS
MDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKT...R...S
RetrocopyMDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKT---RKRRS
ParentalGSSSTRWGGLAWSLERTCATATPPLPTDGSAGKASVWVEGSPSSLSCPTHNSSSGSPSPSRRRHDNRRRS
.SS..................T......GS.........GS.S........SSSGSPSPSRRRHDNRRRS
RetrocopyASSGSSSTRSRSNSTSSSGSSTRTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRS
ParentalRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAY
RSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDH.MEIFSTYGKIKMIDMPVERMHPHLSKGYAY
RetrocopyRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHVMEIFSTYGKIKMIDMPVERMHPHLSKGYAY
ParentalVEFENPDEAEKALKHMDGVFIEMQHFENTAHSAVWAARP-APRRFSPPRRMLPPPPMWRRSPPRMRRRSR
VEFENPDEAEK.LKHMDG..I..Q.F..TA..A.W..RP..PRRFSPPRRMLPPPPMW.RSPPRMRRRSR
RetrocopyVEFENPDEAEKTLKHMDGGQIDGQEFTATAVLAPW-PRP<TPRRFSPPRRMLPPPPMWCRSPPRMRRRSR
ParentalSPRRRSPVRRRSRSPGRRRHRSRSSSNSSR
SPRRRSPVRRRSRSPGRRRHRSRSSSNSSR
RetrocopySPRRRSPVRRRSRSPGRRRHRSRSSSNSSR

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 4 .99 RPM 51 .84 RPM
SRP007412_cerebellum 3 .90 RPM 51 .26 RPM
SRP007412_heart 1 .13 RPM 12 .57 RPM
SRP007412_kidney 1 .23 RPM 21 .83 RPM
SRP007412_liver 0 .71 RPM 13 .27 RPM
SRP007412_testis 2 .18 RPM 27 .66 RPM

ChIP-Seq - click to see more details

Gorilla gorilla was not studied using ChIP-Seq data.

EST - click to see more details

Gorilla gorilla was not studied using EST data.

TSS - click to see more details

Gorilla gorilla was not studied using FANTOM5 data.

Lab - click to see more details

retro_ggor_2016 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_2016 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2911
Pan troglodytes retro_ptro_1967
Parental genes homology:
Parental genes homology involve 25 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178611 retrocopy
retro_amel_194,
Bos taurus ENSBTAG000000099697 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris ENSCAFG000000193971 retrocopy
retro_cfam_449,
Choloepus hoffmanni ENSCHOG000000048664 retrocopies
retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Callithrix jacchus ENSCJAG000000149692 retrocopies
retro_cjac_2127, retro_cjac_3377,
Cavia porcellus ENSCPOG000000020662 retrocopies
retro_cpor_363, retro_cpor_953,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG000000076901 retrocopy
retro_fcat_248,
Homo sapiens ENSG000002059371 retrocopy
retro_hsap_2911,
Gorilla gorilla ENSGGOG00000014275 1 retrocopy
retro_ggor_2016 ,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG000000158911 retrocopy
retro_mdom_1171,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Oryctolagus cuniculus ENSOCUG000000043872 retrocopies
retro_ocun_1544, retro_ocun_1745,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Pan troglodytes ENSPTRG000000313101 retrocopy
retro_ptro_1967,
Pteropus vampyrus ENSPVAG000000051051 retrocopy
retro_pvam_296,
Rattus norvegicus ENSRNOG000000087034 retrocopies
retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,


Copyright © RetrogeneDB 2014-2017