RetrogeneDB ID: | retro_cjac_917 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 11:59826304..59827098(-) | ||
| Located in intron of: | ENSCJAG00000014761 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZNF75D | ||
| Ensembl ID: | ENSCJAG00000014531 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_917
CAGAAATTATGCTATCAGTGGCTGAGGCCAGAGAGCCACTCAAAAAATCAAATCTTGGAAATGGTAGTGCTAGAGCAGTT
CCTGACCATTCTGCCCAAAGAGACCCAGAACTGGGTGCAGAAGCATCATCCACAGCATGTCAAACAGGCTCTGGTCCTGG
TGGAACACTTGCAGAGAGAACCTGGTGAAACAAAGAATGGGGTTGCAGCCCATGAGCTGGGAAAGGAGGCAGTGCTCTTG
GGAGGAACAGCAGTGGGCCCCAGGCTTCAAGTGGAAGCCATCAGAGCCCCAACCAATGGGTCTGTTCCAAAAAGAATATT
GAAATACATACTGGGTACTACAAGAACAGCTGGGCTGGAATACTCTCAAAGAAACCCAGACTGTATATGAAAGAGCTATG
CATGTCCAACAGATTTTAGCCCTTTCTGGGCAGAAAAGCACCAAAGACTGGAAGATAGCATCTGAGCTCATCTGGCCTGA
GTCCCAGAGTTGGTTGACATTTGAAGATGTAGCTGTGTACTTTTCTGAGGAAGAATGGCAATTATTGGATCCTCCTGAGA
AGACTCTACAATGCTGTAATGCAGGATATATCTATGAGACTAGGGTTAAAGCTAAAAAATGACCTTGGAAATGATTATCC
TATGTCTGTTTCTGCATCTGAAATACAAACACCAGGATACAAAGTAACAAAAAAGACCAGAGTGAAAATTGCCCAGAAAA
CAATGGGCAGGGAAAATCATGGTGATACACACAGGGTATAGGAATGGCACCAAGCTTTTCCAAAGAAGAAAAAA
ORF - retro_cjac_917 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.67 % |
| Parental protein coverage: | 52.55 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | QKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLVEFFQRKPDGTKNEVTV |
| QKLC.QWLRPE.HSK.QILEM.VLEQFL.ILPKETQNWVQKHHPQ.VKQALVLVE..QR.P..TKN.V.. | |
| Retrocopy | QKLCYQWLRPESHSKNQILEMVVLEQFLTILPKETQNWVQKHHPQHVKQALVLVEHLQREPGETKNGVAA |
| Parental | HELGKEAVLLGGTAV-APGFKWKPAEPQPTGVFQKEYWNTYWVLQEQLGWNTHKETQPVYERAVHDQQML |
| HELGKEAVLLGGTAV.APGFKWKP.EPQP.G.FQKEY.NTYWVLQEQLGWNT.KETQ.VYERA.H.QQ.L | |
| Retrocopy | HELGKEAVLLGGTAV>APGFKWKPSEPQPMGLFQKEY*NTYWVLQEQLGWNTLKETQTVYERAMHVQQIL |
| Parental | ALSEQKSTKDWKMASEFILPASQSLLTFEDVAVYFSEEEWQLLDPPE-KTLYNDVMQDIYETVISLGLKL |
| ALS.QKSTKDWK.ASE.I.P.SQS.LTFEDVAVYFS.EE...L..P....LYN.VMQDI......LGLKL | |
| Retrocopy | ALSGQKSTKDWKIASELIWPESQSWLTFEDVAVYFS-EEEWQLLDPP>RRLYNAVMQDIS---MRLGLKL |
| Parental | KSDTGNDHPVSVSTSEMQTPGCKVSENTRRKIAQKTMGRENHGDTHRVQKWHRAFPRKKR |
| K.D.GND.P.SVS.SE.QTPG.KV...TR.KIAQKTMGRENHGDTHRV..WH.AFP.KK. | |
| Retrocopy | KNDLGNDYPMSVSASEIQTPGYKVTKKTRVKIAQKTMGRENHGDTHRV*EWHQAFPKKKK |
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 .60 RPM | 0 .51 RPM |
| SRP051959_heart | 2 .49 RPM | 0 .54 RPM |
| SRP051959_kidney | 0 .87 RPM | 0 .89 RPM |
| SRP051959_liver | 1 .19 RPM | 0 .56 RPM |
| SRP051959_lung | 2 .98 RPM | 1 .09 RPM |
| SRP051959_lymph_node | 1 .14 RPM | 2 .92 RPM |
| SRP051959_skeletal_muscle | 0 .63 RPM | 0 .22 RPM |
| SRP051959_spleen | 6 .95 RPM | 1 .37 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_917 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_917 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_917 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014531 | 2 retrocopies |
retro_cjac_3200, retro_cjac_917 ,
|
| Homo sapiens | ENSG00000186376 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000032383 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020747 | 1 retrocopy |