RetrogeneDB ID: | retro_ptro_1123 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 16:74057967..74059009(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMPO | ||
| Ensembl ID: | ENSPTRG00000005331 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_1123
GGGCCGCCGCTCGCCGCCAGCGCCAAAAGAAAGGGGCCCCCGGAATTCTCCAGCTACGTACGAGGAGCGCGAGCCCACAG
CCGTCTCGGCTCCGAGCCCGCCGCCGGCAGGAAAGCCACAAAGAAAACTGATAAACCCAGACAAGATGATAAAGACGATC
TAGATGTAACAGAACTCGCTAATGAAGATCCTTTGGATCAGCTTGTGAAATAGGAGTGAATTGTGGTCCTATTGTGGGAA
CAACCAGGAAGCTGTATGAGAAATAGCTTTTGAAACTGAGGGAGCAAGGAACAGAATCAAGATCGTCTCCTTCAGCAACA
ATTTCTTCTTCAGCAGAAAATACAAGGCAGAATGGAAGTAATGATTCTGACAGATATAGTGACAATGAAGAAGACTCTAA
AATAGAGCTCAAGTTTGAGAAGAGAGAACCGCTAAACAGCGGAGTAAAGACTCCAGTAACCCTCAAGCAAAGAAGAGTTG
AGCACAACGAGAGCTATTCTCAAGCTGGAATAACTGGGACTGAATGGACAAGTGGATCTTCAAAAGGCGGACTTCTGCAG
GCATTATTAACTAGGGAATCTACAAGAGGGTCAAGAAGAACTCCAAGCAAAAGGGTGCACACTTCAGAATATTTTCGTAT
AGATGGAGCAGTAATTTCAGCGAGTACTCCCATAGCTGAAACTATAATTGCTTCAAACAACGAATCCTTAATTGTCAATA
GGGTGACTGGAAATTTCAAGCATGCATTTCCTATTCTGCCAGTCACTGAATTCTCAGACATACCCAGAAGAACACCAAAG
AAACCACTGACAAGAGCTGAAGTGGGAGAAAAAAAACACAGGAAAGAAGAGTAGAAAGGGATATTCTTAAGGAAATGTTC
CCCTATGAAGCAACTACACCAACAAGAATTAGTGCTAGTTGCCGCAGAACAATCAAAGGAGCTGCAGGCCGGCCATTAGA
ACTCAGTGATTTGAGGATGGAGGAGTCGTTTTCATCTACATATCTTCCTAAGTATGTTCCCTTGGCAGATGTCAAGTGAG
AA
ORF - retro_ptro_1123 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.27 % |
| Parental protein coverage: | 75.55 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GPPDFSSDEEREPTPVLGS---GAAAAGR--SRAAVGRKATKKTDKPRQEDKDDLDVTELTNEDLLDQLV |
| GPP.......R...P...S...GA.A..R..S..A.GRKATKKTDKPRQ.DKDDLDVTEL.NED.LDQLV | |
| Retrocopy | GPP-LAASAKRKGPPEFSSYVRGARAHSRLGSEPAAGRKATKKTDKPRQDDKDDLDVTELANEDPLDQLV |
| Parental | K-YGVNPGPIVGTTRKLYEKKLLKLREQGTESRSSTPLPTISSSAENTRQNGSNDSDRYSDNEEDSKIEL |
| K..GVN.GPIVGTTRKLYEK.LLKLREQGTESRSS.P..TISSSAENTRQNGSNDSDRYSDNEEDSKIEL | |
| Retrocopy | K<IGVNCGPIVGTTRKLYEK*LLKLREQGTESRSS-PSATISSSAENTRQNGSNDSDRYSDNEEDSKIEL |
| Parental | KLEKREPLKGRAKTPVTLKQRRVEHNQSYSQAGITETEWTSGSSKGGPLQA-LTRESTRGSRRTPRKRVE |
| K.EKREPL....KTPVTLKQRRVEHN.SYSQAGIT.TEWTSGSSKGG.LQA.LTRESTRGSRRTP.KRV. | |
| Retrocopy | KFEKREPLNSGVKTPVTLKQRRVEHNESYSQAGITGTEWTSGSSKGGLLQALLTRESTRGSRRTPSKRVH |
| Parental | TSEHFRIEGPVISESTPIAETIMASSNESLVVNRVTGNFKHASPILPITEFSDIPRRAPKKPLTRAEVGE |
| TSE.FRI.G.VIS.STPIAETI.AS.NESL.VNRVTGNFKHA.PILP.TEFSDIPRR.PKKPLTRAEVG. | |
| Retrocopy | TSEYFRIDGAVISASTPIAETIIASNNESLIVNRVTGNFKHAFPILPVTEFSDIPRRTPKKPLTRAEVGX |
| Parental | KTEERRVERDI-LKEMFP-YEASTPTGISASCRRPIKGAAGRPLELSDFRMEESFSSKYVPKYVPFADVK |
| ..........I.L....P.YEA.TPT.ISASCRR.IKGAAGRPLELSD.RMEESFSS.Y.PKYVP.ADVK | |
| Retrocopy | XXHRKEE*KGIFLRKCSP<YEATTPTRISASCRRTIKGAAGRPLELSDLRMEESFSSTYLPKYVPLADVK |
| Parental | SE |
| .E | |
| Retrocopy | *E |
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 .02 RPM | 11 .03 RPM |
| SRP007412_cerebellum | 0 .07 RPM | 23 .09 RPM |
| SRP007412_heart | 0 .00 RPM | 8 .60 RPM |
| SRP007412_kidney | 0 .03 RPM | 19 .69 RPM |
| SRP007412_liver | 0 .03 RPM | 18 .69 RPM |
| SRP007412_testis | 6 .53 RPM | 48 .69 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1123 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1123 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1123 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1652 |
| Gorilla gorilla | retro_ggor_1247 |
| Pongo abelii | retro_pabe_1365 |
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000004857 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000005331 | 1 retrocopy |
retro_ptro_1123 ,
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