RetrogeneDB ID: | retro_cjac_266 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:79305649..79306414(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000023314 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PTPLA | ||
| Ensembl ID: | ENSCJAG00000008663 | ||
| Aliases: | None | ||
| Description: | protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A [Source:HGNC Symbol;Acc:9639] |
Retrocopy-Parental alignment summary:
>retro_cjac_266
ATGGCGGCAGCGTCGGCTACTGCAGTGGCGAAGGGGAATGGGGCTGGCAGTGGCCGGGCTGGGGCTGGGGACGCCAGCGG
CACGCAGAAGAAGAAGGGCCTGGGGCCTCTGGTCACGGCATACCTGGTCATCTACAATGAGGTGATGACAGCAGGGTGGC
TGGTTATAGCGGTTGGTCAGGTCCGAGCATACCTGGCTAAGGGTAGCTACCATAGCCTTTATTATTCAATTGAAAAGCCT
TTGAAATTCTTTCAAACTGGAGCCTTATTGGAGGTTTTACATTGTGCTATAGGAATTGTTCCATCTTCTGTTGTCCTGAC
TTCATTCCAGGTGATGTCAAGAGTTTTTCTAATATGGGCAGTAACACACAGCGTCAAAGAGGTACAGACTGAAGACAGTG
TCCTCCTGTTTGTTATTGCCTGGACGATCACGGAAATCATCCGTTACTCCTTTTATACATTCAGTCTATTAAACCATCTG
CCTTACCTCATCAAATGGGCCAGGTACACACTTTTGATTGTGCTGTACCCAATGGGAGTGTCAGGAGAACTGCTCACAAT
ATACGCAGCTCTGCCCTTTGTCAGACAGGCTGGCCTGTATTCCATTAGTTTACCCAACAAATACAATTTCTCTTTTGACT
ACTATGCATTCCTGATTCTAATAATGATCTCCTACATTCCAGTTTTTCCCCAGTTATACTTCCACATGATACACCAGAGA
AGAAAGGTCCTCTCTCATACTGAAGAACACAAGAGATTTGAATAA
ORF - retro_cjac_266 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.32 % |
| Parental protein coverage: | 83.45 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AATMASSDEDGTNGGTSEAGE-DREAPGKRRRLGWLATTWLTFYNIAMTAGWLVLAIAMVRFYMEKGTHR |
| AA..A.....G...G...AG..D.....K...LG.L.T..L..YN..MTAGWLV.A...VR.Y..KG... | |
| Retrocopy | AAASATAVAKGNGAGSGRAGAGDASGTQKKKGLGPLVTAYLVIYNEVMTAGWLVIAVGQVRAYLAKGSYH |
| Parental | GLYKSIQKTLKFFQTFALLEIIHCLIGIVPTSVLVTGVQVSSRIFMVWLITHSIKPIQNEESVVLFLVAW |
| .LY.SI.K.LKFFQT.ALLE..HC.IGIVP.SV..T..QV.SR.F..W..THS.K..Q.E.SV.LF..AW | |
| Retrocopy | SLYYSIEKPLKFFQTGALLEVLHCAIGIVPSSVVLTSFQVMSRVFLIWAVTHSVKEVQTEDSVLLFVIAW |
| Parental | TVTEITRYSFYTFSLLDHLPYFIKWARYNFFIILYPVGVAGELLTIYAALPYVKKTGMFSIRLPNKYNVS |
| T.TEI.RYSFYTFSLL.HLPY.IKWARY...I.LYP.GV.GELLTIYAALP.V...G..SI.LPNKYN.S | |
| Retrocopy | TITEIIRYSFYTFSLLNHLPYLIKWARYTLLIVLYPMGVSGELLTIYAALPFVRQAGLYSISLPNKYNFS |
| Parental | FDYYYFLLITMASYIPLFPQLYFHMLRQRRKVL |
| FDYY.FL...M.SYIP.FPQLYFHM..QRRKVL | |
| Retrocopy | FDYYAFLILIMISYIPVFPQLYFHMIHQRRKVL |
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 |
|---|---|---|
| SRP051959_colon | 1 .91 RPM | 1 .55 RPM |
| SRP051959_heart | 0 .72 RPM | 13 .45 RPM |
| SRP051959_kidney | 2 .88 RPM | 2 .33 RPM |
| SRP051959_liver | 3 .94 RPM | 3 .12 RPM |
| SRP051959_lung | 1 .14 RPM | 2 .78 RPM |
| SRP051959_lymph_node | 1 .00 RPM | 1 .07 RPM |
| SRP051959_skeletal_muscle | 0 .33 RPM | 6 .66 RPM |
| SRP051959_spleen | 0 .57 RPM | 2 .42 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_266 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_266 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_266 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000008663 | 1 retrocopy |
retro_cjac_266 ,
|
| Mus musculus | ENSMUSG00000063275 | 1 retrocopy |