RetrogeneDB ID: | retro_ggor_1614 | ||
Retrocopylocation | Organism: | Gorilla (Gorilla gorilla) | |
| Coordinates: | 22:14581730..14582209(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSGGOG00000023250 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | SDC4 | ||
| Ensembl ID: | ENSGGOG00000004153 | ||
| Aliases: | None | ||
| Description: | Syndecan [Source:UniProtKB/TrEMBL;Acc:G3QNG0] |
Retrocopy-Parental alignment summary:
>retro_ggor_1614
GGGCCAAACTTCTCCAGATCCCTACTGGAAGACTCTGGATGTGGGTGTGGGGGGCAGGAACCTGATGACTCTGAGCTCTC
TGGGTCTGGAGATATTGATGAGTCAAGGGACCCCAAGATCATCCCTGAAGTGATCCAACCCTTGGTGCTTCTAGATAACC
ACATCCCTGAGAGGGCAGGGCCTGGGAACCTGGTCCCACTGAAACCAAGGAACTGGAGGAGAACGAGATCATCCCCAGGA
GGATCTCACCCTCTGCGGGGGACCAGGATGTGTCCAATAAGGCACCCATGTCCAACACTGCCCAGGGCAGCAACATCTTT
GAGAGAATGGAGGTCGTGGCAGTCCTGATTGTGGACAGCATCGCGGGCATCCTCTCTGCTGTTTTCCTGATCCTGCTTCT
GGTGAACCATATGAAGAAGGGTGAAGGCAGAAACGACCTGAGCAGGAAGCCCATCTACAAAAAAGCCCCTAGCAATGAG
GGGCCAAACTTCTCCAGATCCCTACTGGAAGACTCTGGATGTGGGTGTGGGGGGCAGGAACCTGATGACTCTGAGCTCTC
TGGGTCTGGAGATATTGATGAGTCAAGGGACCCCAAGATCATCCCTGAAGTGATCCAACCCTTGGTGCTTCTAGATAACC
ACATCCCTGAGAGGGCAGGGCCTGGGAACCTGGTCCCACTGAAACCAAGGAACTGGAGGAGAACGAGATCATCCCCAGGA
GGATCTCACCCTCTGCGGGGGACCAGGATGTGTCCAATAAGGCACCCATGTCCAACACTGCCCAGGGCAGCAACATCTTT
GAGAGAATGGAGGTCGTGGCAGTCCTGATTGTGGACAGCATCGCGGGCATCCTCTCTGCTGTTTTCCTGATCCTGCTTCT
GGTGAACCATATGAAGAAGGGTGAAGGCAGAAACGACCTGAGCAGGAAGCCCATCTACAAAAAAGCCCCTAGCAATGAG
ORF - retro_ggor_1614 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.81 % |
| Parental protein coverage: | 81.31 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GRYFSGALPDDEDVVGPGQESDDFELSGSGDLDDLEDSMIGPEVIHPLVPLDNHIPERAGSGSQVP-TEP |
| G..FS..L..D......GQE.DD.ELSGSGD.D...D..I.PEVI.PLV.LDNHIPERAG.G..VP.TE. | |
| Retrocopy | GPNFSRSLLEDSGCGCGGQEPDDSELSGSGDIDESRDPKIIPEVIQPLVLLDNHIPERAGPGNLVP<TET |
| Parental | KKLEENEVIPKRISPVEESEDVSNKVSMSSTVQGSNIFERTEVLAALIVGGIVGILFAVFLILLLMYRMK |
| K.LEENE.IP.RISP.....DVSNK..MS.T.QGSNIFER.EV.A.LIV..I.GIL.AVFLILLL...M. | |
| Retrocopy | KELEENEIIPRRISPSAGDQDVSNKAPMSNTAQGSNIFERMEVVAVLIVDSIAGILSAVFLILLLVNHM- |
| Parental | KKDEGSYDLGKKPIYKKAPTNE |
| KK.EG..DL..KPIYKKAP.NE | |
| Retrocopy | KKGEGRNDLSRKPIYKKAPSNE |
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 .00 RPM | 57 .16 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 58 .86 RPM |
| SRP007412_heart | 0 .00 RPM | 24 .05 RPM |
| SRP007412_kidney | 0 .00 RPM | 298 .45 RPM |
| SRP007412_liver | 0 .13 RPM | 224 .08 RPM |
| SRP007412_testis | 0 .00 RPM | 46 .52 RPM |
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_1614 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ggor_1614 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000124145 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000004153 | 1 retrocopy |
retro_ggor_1614 ,
|
| Macropus eugenii | ENSMEUG00000000817 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000006698 | 1 retrocopy |