RetrogeneDB ID: | retro_ptro_3267 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | X:129644114..129645344(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TJAP1 | ||
| Ensembl ID: | ENSPTRG00000018199 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_3267
ATGACCAGTGCAGCCCATGCTAAGAAACCCTACCGTAAGGCACCACCAGAGCATTGGGAGCTGCGACTGGAAATTCCTGG
ATCCAGGTTTGAGCAGGAGGAATCCCTGACTGACTTGGAAAGGATGAAGCTCTCGCAGCAGGATAATGAAGAGCTTCATC
GGCGCCTGGCCTCGGCCACGAGATGCACTGAGGTCCTGGAATGTGAGCTGGAAATTGGGCAGGACTGCCTGGAGCTGGAG
CTGGGCCAGAGCCACGAGGAGCTGGACAAGTTTTAAGGATAAGTTCTGCAGGCTGCAGAACAGCTACATGGCTTCTCAGC
AGACCAACCAGGAGTTGGAGGACAAGCTGCACACACTGCTCAAGAAGGCTGAGATGGATAGGCAGACGCTGGACTGGGAG
ATCGTGGAGCTGACCAACAAGCTGCTGGATGCCAAGAACACCATCAACAAGCTGGAGGAGCTCAACGAGTGGTACCAGGG
GGATTGCAACCTGACTGTGCAGCTCCTCAAGTGCAGCAAGTCCCACTTCCGAAACTATGAGTTCTCCGATCTGTCCTGTG
AGCTACAGGACATGGTTCAGAAACATCTGCATAGTGGTCAAGAGGCCGCCAGCCCTGGTCCTGCTCCCAGCCTAGCCCCA
GCGGCTGTTGTGCCTACTTTGGTCATTGCCCGAGTGTTAGAGAAGCCAGAGTCTCTACTGCTGAATTCAGCCCGGTCAGG
CAGCGCTGGGCACCCCATGGCTGAAGATGTCTTTGTGCATGTGGACATCAGTGAGGGTGCCCCAGGCGATCCAGCCAGTC
CCCCAGCCCCTGGCAGCCCCACCCCCCAACCCAATGGGGAGTGTCACTCTCTGGATACTGTTGGGGGCTCCCCAGAGGAA
GAGCTGCCCCTGCCAGCCTTTGAGAAGCTGAGCCCCTACCCCACCCCATCTCCACCACTCCCACTGTATCCTGGCTGCAG
GGTAATAGAGTTCTCCAAGGATAAAGTTTGGATCCCCTGCAACAGCCCCCTGCCCAACTGCACTTACACTACCCGCCAGG
CCATTTCGCTGAGCCTGGTGGGGGAAGGGAGTGAGCGGGCCTGCCCCAGCCCAGTGCTCAGCGCCCCTGCCTCAGCCTAG
GCCTCACTCAACCACCAGCTCAGCTCAGTGCCCCCACACTCAGTGCCCCAGCCCAGTCTGTTAGCTCTGAAAAGGACCTG
CTGGGCAGCTGGCAGTGGGCATTTGTGGAC
ORF - retro_ptro_3267 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.04 % |
| Parental protein coverage: | 74.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MTSAAPAKKPYRKAPPEHRELRLEIPGSRLEQEEPLTDAERMKLLQQENEELRRRLASATRRTEALEREL |
| MTSAA.AKKPYRKAPPEH.ELRLEIPGSR.EQEE.LTD.ERMKL.QQ.NEEL.RRLASATR.TE.LE.EL | |
| Retrocopy | MTSAAHAKKPYRKAPPEHWELRLEIPGSRFEQEESLTDLERMKLSQQDNEELHRRLASATRCTEVLECEL |
| Parental | EIGQDCLELELGQSREELDKF-KDKFRRLQNSYTASQRTNQELEDKLHTLIKKAEMDRKTLDWEIVELTN |
| EIGQDCLELELGQS.EELDKF.KDKF.RLQNSY.ASQ.TNQELEDKLHTL.KKAEMDR.TLDWEIVELTN | |
| Retrocopy | EIGQDCLELELGQSHEELDKF>KDKFCRLQNSYMASQQTNQELEDKLHTLLKKAEMDRQTLDWEIVELTN |
| Parental | KLLDAKNTINKLEELNERYRLDCNLAVQLLKCNKSHFRNHKFADLPCELQDMVRKHLHSGQEAASPGPAP |
| KLLDAKNTINKLEELNE.Y..DCNL.VQLLKC.KSHFRN..F.DL.CELQDMV.KHLHSGQEAASPGPAP | |
| Retrocopy | KLLDAKNTINKLEELNEWYQGDCNLTVQLLKCSKSHFRNYEFSDLSCELQDMVQKHLHSGQEAASPGPAP |
| Parental | SLAPGAVVPTSVIARVLEKPESLLLNSAQSGSAGRPLAEDVFVHVDMSEGVPGDPASPPAPGSPTPQPNG |
| SLAP.AVVPT.VIARVLEKPESLLLNSA.SGSAG.P.AEDVFVHVD.SEG.PGDPAS............G | |
| Retrocopy | SLAPAAVVPTLVIARVLEKPESLLLNSARSGSAGHPMAEDVFVHVDISEGAPGDPASXXXXXXXXXXXXG |
| Parental | ECHSLGTARGSPEEELPLPAFEKLNPYPTPSPPHPLYPGRRVIEFSEDKVQIPRNSPLPNCTYATRQAIS |
| ECHSL.T..GSPEEELPLPAFEKL.PYPTPSPP.PLYPG.RVIEFS.DKV.IP.NSPLPNCTY.TRQAIS | |
| Retrocopy | ECHSLDTVGGSPEEELPLPAFEKLSPYPTPSPPLPLYPGCRVIEFSKDKVWIPCNSPLPNCTYTTRQAIS |
| Parental | LSLVEEGSERARPSPVPSTPASAQASPHHQPSPAP-LTLSAPASSASSEEDLLVSWQRAFVD |
| LSLV.EGSERA.PSPV.S.PASA.AS..HQ.S..P..TLSAPA.S.SSE.DLL.SWQ.AFVD | |
| Retrocopy | LSLVGEGSERACPSPVLSAPASA*ASLNHQLSSVP<PTLSAPAQSVSSEKDLLGSWQWAFVD |
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 .07 RPM | 63 .53 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 35 .49 RPM |
| SRP007412_heart | 0 .00 RPM | 10 .73 RPM |
| SRP007412_kidney | 0 .00 RPM | 31 .51 RPM |
| SRP007412_liver | 0 .00 RPM | 21 .77 RPM |
| SRP007412_testis | 0 .00 RPM | 16 .76 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3267 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3267 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_3267 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4899 |
| Gorilla gorilla | retro_ggor_3059 |
| Pongo abelii | retro_pabe_3811 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000137221 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000015185 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000016642 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000018199 | 1 retrocopy |
retro_ptro_3267 ,
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