RetrogeneDB ID:

retro_ggor_335

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:1:189222713..189223885(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TFDP1
Ensembl ID:ENSGGOG00000004908
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_335
ATGGCAAAAGTTGCTGGTCTAATTGAAGCAAACGGAGAACTCAAGGTCTTCATAGACCAGAACCTTAGTCCCGGAAAAGG
CATTGGTGTCCCTCATGGCCGTTCACCCCTCCATCGTCAGCCCGCTCGGGAAGCAGCTCTTGCCGAAAACCTTTGGACAG
TCCAATATCAACGTTGTCCCGCAAGTGGTAACCGGTACGCCTCAGAGACCGGCAGCGTCAAACACCCTCGTGATAGGTAG
CCCACACACCGCCAGCACTCACTTTGCCTCTCAGAACCAGCCTTCCGACTCCTCACCTTGGTCTGCCGGGAAGTGCAACA
GGAAAGGAGAGAAGAATGGCAAGGCCTGTGGCATTTCTCCAGGAAGGTCTGAGACAAGGTGCAGTGGAAAGGGACCACTT
CCTATCACGAGGTGGCGGACGAGCTGGCAGAGGAATTCAGTGCTGCCAGCAACCACATCTTACCAAGCGAGTCAGCTTAT
GACCAGAGCAACATCGACGGCGCGTCTACTATGCCTTAAACGTGCTGATGGCCATGAATATCTCCAAGGAGAAGAAGGAG
ATCAAGTGAGTTGGTCTGCCCACCAACTCGGCTCAGGAATGTCAGAACTCAGAGGTGGAAAGACAGAGGAGACTTGACAG
AATAAAACAGAAAATCTCAATTTCAGAAACTTATTTGACAGTAAATTGCCTTCAAGAACCTGGTGAAGAGAGAAACCAGC
ACGCGGAGCAGCAGGCCAGCCAGCCAACGACGCCCAGCTGGCTCATCCACCTGCCCTTCATCATCGTTAACACCAGCAAG
AAGACCGTCATCGACTGCAGCATCTCCAACGACAAATTCGAGTATCTGTTTAATTTTGACAACACATCTGAAATCTACAA
TGACATAGAAGTGCTGAAGCGGATGAGCATGGCTTGTGGGCTGGAGTCCGGGAGCTTCTCTGCTGAGGACCTTAAAATGG
CCAGAAGTCTGGTCCCAAAGGCTCTGGAGCCGTACGTGACAGAAATGGCTCAGGGAACTGTCGGAGGCGTGTTCATCACG
ACGGCACGTTCCATGTCTAACGGCAAGAAGCTCTCTGCCAGTGACCTGACCAATGGTGTGGATGAGATACTGGCCACAAG
CTCCAACCTCAGTACAATGGCTCCGGGGCGGAGGCCCCGGTGTCCTACGTCG

ORF - retro_ggor_335 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.49 %
Parental protein coverage: 98.49 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAKDAGLIEANGELKVFIDQNLSPGKGV-VSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQR
MAK.AGLIEANGELKVFIDQNLSPGKG..VSL.AVHPS.V.PLGKQLLPKTFGQSN.N...QVV.GTPQR
RetrocopyMAKVAGLIEANGELKVFIDQNLSPGKGI>VSLMAVHPSIVSPLGKQLLPKTFGQSNINVVPQVVTGTPQR
ParentalPAASNTLVVGSPHTPSTHFASQNQPSDSSPWSAGKRNRKGEKNGK-GLRHFSMKVCEKVQRKGTTSYNEV
PAASNTLV.GSPHT.STHFASQNQPSDSSPWSAGK.NRKGEKNGK.GL.HFS.KV..KVQ.KGTTSY.EV
RetrocopyPAASNTLVIGSPHTASTHFASQNQPSDSSPWSAGKCNRKGEKNGK<GLWHFSRKV*DKVQWKGTTSYHEV
ParentalADELVAEFSAADNHILPNESAYDQKNI-RRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEV
ADEL..EFSAA.NHILP.ESAYDQ.NI.RRRVY.ALNVLMAMNI.SKEKKEIK..GLPTNSAQECQN.EV
RetrocopyADELAEEFSAASNHILPSESAYDQSNI<RRRVYYALNVLMAMNI-SKEKKEIK*VGLPTNSAQECQNSEV
ParentalERQRRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSIS
ERQRRL.RIKQK.S.................RN.HAEQQAS.P..P...IHLPFIIVNTSKKTVIDCSIS
RetrocopyERQRRLDRIKQKISISETYLTVNCLQEPGEERNQHAEQQASQPTTPSWLIHLPFIIVNTSKKTVIDCSIS
ParentalNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFI
NDKFEYLFNFDNT.EI..DIEVLKRM.MACGLESGS.SAEDLKMARSLVPKALEPYVTEMAQGTVGGVFI
RetrocopyNDKFEYLFNFDNTSEIYNDIEVLKRMSMACGLESGSFSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFI
ParentalTTAGSTSNGTRFSASDLTNGADGMLATSSNGSQYS-GSRVETPVS
TTA.S.SNG...SASDLTNG.D..LATSSN.S....G.R...P.S
RetrocopyTTARSMSNGKKLSASDLTNGVDEILATSSNLSTMAPGRRPRCPTS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .00 RPM 23 .69 RPM
SRP007412_cerebellum 0 .04 RPM 35 .18 RPM
SRP007412_heart 0 .00 RPM 6 .91 RPM
SRP007412_kidney 0 .00 RPM 17 .09 RPM
SRP007412_liver 0 .00 RPM 11 .71 RPM
SRP007412_testis 9 .12 RPM 46 .21 RPM
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_335 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_335 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_299
Pongo abelii retro_pabe_378

Parental genes homology:
Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000044678 retrocopies
Callithrix jacchus ENSCJAG000000069502 retrocopies
Homo sapiens ENSG000001981764 retrocopies
Gorilla gorilla ENSGGOG00000004908 2 retrocopies
retro_ggor_17, retro_ggor_335 ,
Loxodonta africana ENSLAFG000000079271 retrocopy
Myotis lucifugus ENSMLUG000000121651 retrocopy
Macaca mulatta ENSMMUG000000074231 retrocopy
Mus musculus ENSMUSG000000384822 retrocopies
Nomascus leucogenys ENSNLEG000000008493 retrocopies
Otolemur garnettii ENSOGAG000000035321 retrocopy
Pongo abelii ENSPPYG000000258893 retrocopies



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