RetrogeneDB ID: | retro_mmul_1194 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 15:72102807..72103953(-) | ||
| Located in intron of: | ENSMMUG00000014558 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TCF3 | ||
| Ensembl ID: | ENSMMUG00000009017 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mmul_1194
GCCTCCTTTGGGAGAGACGCAGGCGTGGGCGGCCTGACTCAGGCTGGCTTCCTGCCGGGCGAGCTGGCCCTCAGCAGCCC
CGGACCCCTGTTCCCTTTGGGCATGAAGGCGACCTCCCAGTACTACCCCTCCTACGCCGGCAGCTCCGGCGGAGAGAGGC
GGACGGCGGCCTGGACACGCAGTCCACAAAGGTCCAGAAGGTCCTGCCTGTCTTCCATCCTCGGCGTACCTGCCCAGCTC
AGGTGAGGACTACGGTAGGGATGCCGCCGCCTACCTGTCCGCCAAGACCCCCAGCAGGGCCTATCCCGCCCCCTTCTACA
TGGCAGATGGCAGGCAGCATACACCCCTCAGCCCCTCAGCCGAGGTCTGGTGTTGCCCGGGTCAGGCGGGCTTTGGCCCC
ATGCTGGGTGGGGGCTCATACCCCCCGCCTCTCCCGCCCAGCAGCTGCCCTGTGGGCAGTGGCAGAGGCAGCAGCACATT
TGGTGGCCTGCACCAGCACGAGCGCATGGGCTACCAGCTGCACAGAGCAGAGGTGAACGGTGGTCTCCCAGCTGCATCCA
CCTTCTCCTTGGCCCCCTGGAGCTGGAGCGTCTCCAGCCACAGGCCACCTGTCAGCGGGGCCAACATATTCCTGGGCTCG
CGAGGGACCACAGCTGGCAGCTCCTGGGACGCCCTCAGGCAGGCATGTCCTCAATCTACTCCCCGGATCACTCAAGCAAT
AGCTTCTCGTCCAGCTCCTCCACTGCTGTGGGCTACCCCCAGGGTCTGGGAGGGATGTCGCACTGGCCCGGAACAGGAGT
CCCCGGTGCCTTATCACCCAGCTACGACGGGGATTTCCATGGCGTGCAGAGTAAGACAGAAGACCACCTGAACAAGGCCA
TCCACGTGCTCTGCAGCCACACCGTGGGCACGGCCGGCAATGGGCCCACGCTGCTGCCCGGCCACAGGGCGCTGGCTTAG
GCTTCGCCGGCCCTATGCTGCTAGTGGGGGCAGCACGCAGGCCTGGTCAGAGGCTGACACCCTGAGGACGGCCCTGTGGG
CAGCGCCAGCCTCATGCACATCCACGTGGCCCTCTCCAGCTAGCCAGGCGCCCTCTCCGACCTCTCTTGGCCTCCCGACT
CCTACAGTGGGCTAGGGCAAGCAGGC
ORF - retro_mmul_1194 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.64 % |
| Parental protein coverage: | 58.71 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | ASFGRDAGVGGLTQAGFLSGELALSSPGPLSPSGMKGTSQYYPSYSGSS-RRRAADGSLDTQPKKVRKV- |
| ASFGRDAGVGGLTQAGFL.GELALSSPGPL.P.GMK.TSQYYPSY.GSS.RRR.ADG.LDTQ..KV.KV. | |
| Retrocopy | ASFGRDAGVGGLTQAGFLPGELALSSPGPLFPLGMKATSQYYPSYAGSS<RRREADGGLDTQSTKVQKV< |
| Parental | PPGLPSSVYPPSSGEDYGRDAAAYPSAKTPSSAYPAPFYMADGSLH----PSAELWSPPGQAGFGPMLGG |
| P..LPSS.Y.PSSGEDYGRDAAAY.SAKTPS.AYPAPFYMADG..H....PSAE.W..PGQAGFGPMLGG | |
| Retrocopy | PACLPSSAYLPSSGEDYGRDAAAYLSAKTPSRAYPAPFYMADGRQHTPLSPSAEVWCCPGQAGFGPMLGG |
| Parental | GSSPLPLPPGSGPVGSSGSSSTFAGLHQHERMGYQLHGAEVNGGLPAASSFSSAPGATYGGVSSHTPPVS |
| GS.P.PLPP.S.PVGS...SSTF.GLHQHERMGYQLH.AEVNGGLPAAS.FS.AP......VSSH.PPVS | |
| Retrocopy | GSYPPPLPPSSCPVGSGRGSSTFGGLHQHERMGYQLHRAEVNGGLPAASTFSLAPWSW--SVSSHRPPVS |
| Parental | GADSLLGSRGTTAGSSGDALGKA-LASIYSPDHSSNNFSSSPSTPVGSPQGLAGTSQWPRAGAPGALSPS |
| GA...LGSRGTTAGSS.DAL..A...SIYSPDHSSN.FSSS.ST.VG.PQGL.G.S.WP..G.PGALSPS | |
| Retrocopy | GANIFLGSRGTTAGSSWDALRQA<MSSIYSPDHSSNSFSSSSSTAVGYPQGLGGMSHWPGTGVPGALSPS |
| Parental | YDGGLHGLQSKIEDHLDEAIHVLRSHAVGTAGDMHTLLPGHGALA-SGFAGPMSL-GGRHAGLVGGGHPE |
| YDG..HG.QSK.EDHL..AIHVL.SH.VGTAG...TLLPGH.ALA..GFAGPM.L..G.HAGLV.G.HPE | |
| Retrocopy | YDGDFHGVQSKTEDHLNKAIHVLCSHTVGTAGNGPTLLPGHRALA<LGFAGPMLL>WGQHAGLVRG*HPE |
| Parental | DGLAGSTSLMHNHAALPSQPGALPDLSRPPDSYSGQGRAG |
| DG..GS.SLMH.H.AL.S.PGAL.DLS.PPDSYSG.G.AG | |
| Retrocopy | DGPVGSASLMHIHVALSS*PGALSDLSWPPDSYSGLGQAG |
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 | 0 .00 RPM | 3 .03 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .16 RPM | 9 .52 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .71 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .12 RPM |
| SRP007412_kidney | 0 .00 RPM | 5 .63 RPM |
| SRP007412_liver | 0 .20 RPM | 8 .51 RPM |
| SRP007412_testis | 0 .04 RPM | 22 .35 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1194 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1194 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_1194 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4123 |
| Gorilla gorilla | retro_ggor_2770 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000071564 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000003667 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000009017 | 1 retrocopy |
retro_mmul_1194 ,
|
| Nomascus leucogenys | ENSNLEG00000001742 | 1 retrocopy |