RetrogeneDB ID: | retro_cjac_407 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:70700610..70701372(+) | ||
| Located in intron of: | ENSCJAG00000033311 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FOXN3 | ||
| Ensembl ID: | ENSCJAG00000017620 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_407
GTGGACAAGGAGAGGAGTCAGAGTCGTTGTGGTGGAAAAGGGTCGTTGTGGTGCATAGACCCACAGTATAGATAAAACTT
AATTCAGGCTTTGAAAAAGACACCTTATAACCCACACCCACACGTGTTTAATACACCTCCCACCTGTCCTCAGGCATATC
AAAGCACATCAGGTCCACCCATATGGCCGGGCAGTACCTTCTTCAAGAGAAACGGAGCCCTTCTCCAAGTTCCTCCAGAA
GTGATCCAAAATGGAGCGCGAGTCCTGAGCCGAAGGCTGTTTCCTGGCGTGTGGCCGCTGCCCATCACTCCCACTGGGGT
GACAGCGGCCATGAGGAACGGCATCACCAGCTGCTGGATATGGACTGAGATCGAGCCGTCGTGCTGCTCCCCCGTGGTCA
GCAGAGACCCCAACGAGGATCACAACTACAGCAGTGCCAAGTCCTCCAATGTCCCGAGCACCTCTCCCACCAGCGACTCC
ATCTCCTCCTCTTCCTCCTCCTCCTCCTCCTCCGACCACTACGAGTTTGCCACCAAGAGGAGCCAGGAGGGCAGCGAGGG
GAGATGCTGGAGCCACGAGAGCCACAGTGACACTGAAGAAAACGACAGGAAGCACAGCCAAAAGGAGCCCAAGGATGCTC
TGGGGGACAGTGGGTATGCATCCCAGCACAAGAAGCGCCAGCACTTCGCCAAGGCCAGAAGGGTCCCCAGCGACACACTG
CCCCTCAAAAAGAGACGCACCGAAAAGCCCCCCGAGAGCGAC
ORF - retro_cjac_407 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.16 % |
| Parental protein coverage: | 54.16 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VDKERSQSI--GKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKR |
| VDKERSQS...GKGSLWCIDP.YR.NLIQALKKTPY.PHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKR | |
| Retrocopy | VDKERSQSRCGGKGSLWCIDPQYR*NLIQALKKTPYNPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKR |
| Parental | NGALLQVPPGVIQNGARVLSRGLFPGVRPLPITPIGVTAAMRNGITSCRMRTESEPSCGSPVVSGDPKED |
| NGALLQVPP.VIQNGARVLSR.LFPGV.PLPITP.GVTAAMRNGITSC...TE.EPSC.SPVVS.DP.ED | |
| Retrocopy | NGALLQVPPEVIQNGARVLSRRLFPGVWPLPITPTGVTAAMRNGITSCWIWTEIEPSCCSPVVSRDPNED |
| Parental | HNY-SSAKSSNVRSTSPTSDSISSSSSSSADDHYEFATKGSQEGSEGSEGSFRSHESHSDTEEDDRKHSQ |
| HNY.S...S......................DHYEFATK.SQ...EGSEG...SHESHSDTEE.DRKHSQ | |
| Retrocopy | HNYSSAKSSNVPSTSPTSDSXXXXXXXXXXXDHYEFATKRSQ---EGSEGRCWSHESHSDTEENDRKHSQ |
| Parental | KEPKDALGDSGYASQHKKRQHFAKARRVPSDTLPLKKRRTEKPPESD |
| KEPKDALGDSGYASQHKKRQHFAKARRVPSDTLPLKKRRTEKPPESD | |
| Retrocopy | KEPKDALGDSGYASQHKKRQHFAKARRVPSDTLPLKKRRTEKPPESD |
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 | 0 .00 RPM | 13 .53 RPM |
| SRP051959_heart | 0 .00 RPM | 37 .80 RPM |
| SRP051959_kidney | 0 .00 RPM | 14 .22 RPM |
| SRP051959_liver | 0 .00 RPM | 22 .05 RPM |
| SRP051959_lung | 0 .00 RPM | 26 .04 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 21 .28 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 26 .80 RPM |
| SRP051959_spleen | 0 .00 RPM | 37 .08 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_407 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_407 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_407 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 | ENSCJAG00000017620 | 1 retrocopy |
retro_cjac_407 ,
|
| Nomascus leucogenys | ENSNLEG00000016989 | 1 retrocopy |