RetrogeneDB ID: | retro_ptro_1728 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 2B:196543400..196544416(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DNAJB1 | ||
| Ensembl ID: | ENSPTRG00000010594 | ||
| Aliases: | None | ||
| Description: | DnaJ (Hsp40) homolog, subfamily B, member 1 [Source:HGNC Symbol;Acc:5270] |
Retrocopy-Parental alignment summary:
>retro_ptro_1728
GTGGGCAAAGACTACTACCAGACGCTGGGCCTGGCCCGCGGCGCGTCAGACGAGGAGATCAAGCGGGCCTACCGCCGCCA
GGTGCTGCGCTACCACCCAGACAAGAACAAGGAGCCCGGCGCCGAGGAGAAGTTCAAGGAGATCGCCGAGGCCTATGAGG
TGCTCAGAGACCCGCGCAAGCGCGAGATCTTCGACCGCTACCGGGAGGAAGCCCTAAAGGGCAGCGGCCCCAGTGGCGGT
AGCGGCGGTGGTGCCAATGCTACCTCTTTCAGCTACACATTCCATGGAGACCCTCTTGCCATGTTTGCTGAGTTCTTCGG
TGGCAAAAATCCCTTTGACACCTTTTTTGGGCAGCGGAACGGGGAGGAAGTCATGGACATTGCTGACCCATTCTCTGGCT
TCCCTATGGGAATGGGTGGCTTCACCAACATGAACTTTGGCCGCTCCCGCCCTGCCCAGGAGCCCACCCGAAAGAAGCAA
GATCCCCCAGTCACCCACGACCTTCGAGTCTCCCTTGAAGAGATCTACAGCGGTTGTACCAAGAAGATGAAAATCTCCCA
CAAGCGGCTAAACCCCGACGGAAAGAGCATTCGAAACGAAGACAAAATCTTGACCATCGAAGTGAAGAAGGGGTGGAAAG
AAGGGACCAAGATCACCTTCCCCAAAGAAGGAGACCAGACCTCCAACAACATTCCAGCTGATATCGTCTTTGTTTTAAAG
GACAAGCCACACAATATCTTTAAGAGAGATGGTTCTGATGTCATTTATCCTTCCAGGATCAGCCTCCCGGAGGCTCTGTG
TGGCACACAGTGAACGTCCCCACTCTGGACGGCAGGACCATTCCCGTCGTGTTCAAAGATGCCATCAGGCCTGGCATGCG
ACGAAAAGTTCGTGGAGAAGGCCTTCCCCTCCCCAAAACGCCAGAGAAACGTGGGGACCTCATTATTGAATTGGAAGTGA
TCTTCCCCAAAAGGATTCCCCAGACATCAAGAACCGTACTTGAGCAGATTCTTCCA
ORF - retro_ptro_1728 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.94 % |
| Parental protein coverage: | 99.7 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MGKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYR-- |
| .GKDYYQTLGLARGASDEEIKRAYRRQ.LRYHPDKNKEPGAEEKFKEIAEAY.VL.DPRKREIFDRYR.. | |
| Retrocopy | VGKDYYQTLGLARGASDEEIKRAYRRQVLRYHPDKNKEPGAEEKFKEIAEAYEVLRDPRKREIFDRYREE |
| Parental | -LKGSGPSGGSGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGG |
| .LKGSGPSGGSGGGAN.TSFSYTFHGDP.AMFAEFFGG.NPFDTFFGQRNGEE.MDI.DPFSGFPMGMGG | |
| Retrocopy | ALKGSGPSGGSGGGANATSFSYTFHGDPLAMFAEFFGGKNPFDTFFGQRNGEEVMDIADPFSGFPMGMGG |
| Parental | FTNVNFGRSRSAQEPARKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKK |
| FTN.NFGRSR.AQEP.RKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKK | |
| Retrocopy | FTNMNFGRSRPAQEPTRKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKK |
| Parental | GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGC-TVNVPTLDGR |
| GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYP.RISL.EALCG..TVNVPTLDGR | |
| Retrocopy | GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPSRISLPEALCGT<TVNVPTLDGR |
| Parental | TIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLP |
| TIPVVFKD.IRPGMRRKV.GEGLPLPKTPEKRGDLIIE.EVIFP.RIPQTSRTVLEQ.LP | |
| Retrocopy | TIPVVFKDAIRPGMRRKVRGEGLPLPKTPEKRGDLIIELEVIFPKRIPQTSRTVLEQILP |
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 .14 RPM | 61 .18 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 44 .77 RPM |
| SRP007412_heart | 0 .15 RPM | 81 .43 RPM |
| SRP007412_kidney | 0 .68 RPM | 208 .64 RPM |
| SRP007412_liver | 0 .36 RPM | 164 .91 RPM |
| SRP007412_testis | 3 .16 RPM | 415 .32 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1728 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1728 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1728 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Pongo abelii | retro_pabe_2136 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004666 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000009647 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000010594 | 1 retrocopy |
retro_ptro_1728 ,
|
| Rattus norvegicus | ENSRNOG00000021824 | 1 retrocopy |