RetrogeneDB ID: | retro_ptro_1055 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 15:51313448..51314766(-) | ||
| Located in intron of: | ENSPTRG00000007093 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IFT80 | ||
| Ensembl ID: | ENSPTRG00000015578 | ||
| Aliases: | None | ||
| Description: | intraflagellar transport 80 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:29262] |
Retrocopy-Parental alignment summary:
>retro_ptro_1055
AAAGTATCTTTGAACTCTGCACACTTAGTTGTTTCAATGTCTCTTCAATGTTATGTGGTCTCCACAAAGAACTGGAATAC
ACCAATTATATTTGATCTCAAAGAAGGAACAGTTAGTTTTATCCTGCAGGCAGAAAGACATTTTCTTCTTGTAGATGTTA
GTAGTATCGATTTATATTCATATGAAGGGCCCTTTATTTCATCTCCAAAATTTCCTGCAGTGAGAACAGATATTCTGAAT
GCACAGACTGTGTCTCTGAGTAATGATACCATAGCAATGAGACAAAGCTGATGAAAAAATAATCTTTTTCTTCAAGGTAT
CAACTGGAAAACTATTAGATGATGGAAAGCTTCTTCCTCGTAAGGATGCAATCTTGAAAATTGCTCTGGATCAAAAAGGA
CTTACCAATGACAGAAAAGTCACTTTCATTGATAAAAATAGAGATATCTATATCACTTCTGTGAAACAATTTGGGAAGGA
AGAAAAAATTCTCAAACTTGGAACAATGGTGCATACTTTGGCATGGAGTGATACATGCAATGTCCTTTGCAGGCTTCAGG
ATACTCAATTTACAGTGTGGTATTATTCCAATATGGTTTATGTGGACAGTGACACTTTGCCTAAAACATTACATGAAAGG
GATACAAATAAATTCAGTAAAAATTCCCAAATTGTGAGTTTTCTTGGAAATCAGGTAACTATAACAAGAGTTAACGGCCC
TCTGGTTCACATCAGTGTATCACCATATCCTGTTATTCTCCCTGAATATGTAGGCAGTTCAAAATGGGAAGATGATGTAA
GACTTTGCTGCTTTGTTAAGGAGCAAACCATGTGAGCTTGTCTACCTGCTATGGCAGTTGCTAATCAAAATATTACTATT
ACAGAAATAGGCTATGCAGCAATTGGTGAAATTGATAAGTTTCAGTACATCAATTCTATAAAAAGTCTTTCATTTAAAGA
GTCAAAAAATGGTCCACATACTAAAGTTTAGTGGAAACATACAGGAGGCTGAAATAGCACTTCTTCAGGCTGGCCTCATT
GTCAAGCAATCCAGATCAATATTAATCTCTGCAACTGAAAAGGGCACTGGAATTGGCTGCAAAATACAAAACACATGTTG
ATACGGTTGTTGCTTAGTGTCAAAAGAAAAGTTTTTGGAGACATTTGGTAAAGAGGAAACATAAACAATACTTGCAGCAT
GCAGAAGGTCTCCAAATAGATTGAGAGAAAAATCAAAGCCAAAATTGGGATTGAAATTACAAAAGAAGGAGAACAATCAT
CAAGCAGCCAATCCAGTAAGAGTATGAGTCTAAAGCCC
ORF - retro_ptro_1055 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.05 % |
| Parental protein coverage: | 56.44 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | KASLNYAHLVVSTSLQCYVFSTKNWNTPIIFDLKEGTVSLILQAERHFLLVDGSSIYLYSYEGRFISSPK |
| K.SLN.AHLVVS.SLQCYV.STKNWNTPIIFDLKEGTVS.ILQAERHFLLVD.SSI.LYSYEG.FISSPK | |
| Retrocopy | KVSLNSAHLVVSMSLQCYVVSTKNWNTPIIFDLKEGTVSFILQAERHFLLVDVSSIDLYSYEGPFISSPK |
| Parental | FPGMRTDILNAQTVSLSNDTIAIRDK-ADEKIIFLFEASTGKPLGDGKFLSHKNEILEIALDQKGLTNDR |
| FP..RTDILNAQTVSLSNDTIA.R.......I.F.F..STGK.L.DGK.L..K..IL.IALDQKGLTNDR | |
| Retrocopy | FPAVRTDILNAQTVSLSNDTIAMRQS>DEKIIFF-FKVSTGKLLDDGKLLPRKDAILKIALDQKGLTNDR |
| Parental | KIAFIDKNRDLCITSVKRFGKEEQIIKLGTMVHTLAWNDTCNILCGLQDTRFIVWYYPNTVYVDRDILPK |
| K..FIDKNRD..ITSVK.FGKEE.I.KLGTMVHTLAW.DTCN.LC.LQDT.F.VWYY.N.VYVD.D.LPK | |
| Retrocopy | KVTFIDKNRDIYITSVKQFGKEEKILKLGTMVHTLAWSDTCNVLCRLQDTQFTVWYYSNMVYVDSDTLPK |
| Parental | TLYERDASEFSKNPHIVSFVGNQVTIRRADGSLVHISISPYPAILHEYVSSSKWEDAVRLCRFVKEQTMW |
| TL.ERD...FSKN..IVSF.GNQVTI.R..G.LVHIS.SPYP.IL.EYV.SSKWED.VRLC.FVKEQTM. | |
| Retrocopy | TLHERDTNKFSKNSQIVSFLGNQVTITRVNGPLVHISVSPYPVILPEYVGSSKWEDDVRLCCFVKEQTM* |
| Parental | ACLAAMAVANRDMTTAEIAYAAIGEIDKVQYINSIKNLPSKES-KMAHILLFSGNIQEAEIVLLQAGLVY |
| ACL.AMAVAN...T..EI.YAAIGEIDK.QYINSIK.L..KES.KM.HIL.FSGNIQEAEI.LLQAGL.. | |
| Retrocopy | ACLPAMAVANQNITITEIGYAAIGEIDKFQYINSIKSLSFKES>KMVHILKFSGNIQEAEIALLQAGLIV |
| Parental | -QAIQININLYN-WERALELAVKYKTHVDTVLAYRQKFLETFGKQETNKRYLHY---AEGLQIDWE-KIK |
| .QAIQININL.N...RALELA.KYKTHVDTV.A..QK....F...........Y...AEGLQID.E.KIK | |
| Retrocopy | <QAIQININLCN<LKRALELAAKYKTHVDTVVA*CQK--KSFWRHLVKRKHKQYLQHAEGLQID*E>KIK |
| Parental | AKIEMEITKEREQ-SSSQSSKSIGLKP |
| AKI..EITKE.EQ.SSSQSSKS..LKP | |
| Retrocopy | AKIGIEITKEGEQSSSSQSSKSMSLKP |
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 | 7 .58 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 6 .02 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .35 RPM |
| SRP007412_kidney | 0 .03 RPM | 7 .74 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .19 RPM |
| SRP007412_testis | 0 .00 RPM | 60 .38 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1055 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1055 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1055 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1568 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000068885 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000017282 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014255 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000015578 | 2 retrocopies |
retro_ptro_1055 , retro_ptro_2951,
|