RetrogeneDB ID: | retro_eeur_195 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_204842:8414..9222(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM76B | ||
| Ensembl ID: | ENSEEUG00000008119 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 76, member B [Source:HGNC Symbol;Acc:28492] |
Retrocopy-Parental alignment summary:
>retro_eeur_195
GCCTGCACCAAGTGCACCCAGCGCTACCCCTTTGAGGAACTCTCCTAGGGCCAGCAGCTCTGCAAGGAATGTCGGATTGT
GCACCAGATCATCGTCAAGTGCACCTACTGCAGGTCGGAGTTCCAGCAGGAGAGCAAAACTAACACAATTTGTAAGAAGT
GTGCTCAAAATGTGAAACAGTTTGGCACGCCCAAGCCTTATCAGTACTGTAACATAATCGCAGCATTCATTGGCACAAAG
TGTCAGAGATGCACAAATTTAGAGAAAAAGTACGGACCGCCTCAGACCTGCGAGCAGTGCAAGCAGTAGTGTGCTTTCGA
TCGGAAAGAAGAAGGAAGAAGAAAGGTTGATGGGAAGTTGTTGTGCTGGCTCTACTTTATCATACAAGAGAGTTTTACAG
AAGACAAAAGAACAGAGGAAGAGCCTGGGATGTCACATTCAAATTCCTCTTCTTTCATCCCTCACCAAGAAAGACCAGCA
TCAGTCAAAGCACAATCACCACCACCACCACCATCACCACCATCACAGCAGTAGCCATCACAAAATTAGCAACCTGAGTC
CAGAACAAGAGCAGGGACTGTGGAAACAGAGCCATAAATCCTCTGCAACAATTGAGAATGAAACTCCAAAGAAAAAGCCC
AAATTGGAATCTAAGCCATCTAATGGAGATAGTAACTCTATAAATCAGTCAGCAGATAGTGGGGGAACAGACAGTTTTGT
CCTCATAAGTCAACTGAAGGAAGAAGTGACATCACTTAAGTGTCTCTTACAGCAGAGAGACCAGGCCATCTTAGAGAAAG
ATAAAAAG
ORF - retro_eeur_195 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.17 % |
| Parental protein coverage: | 97.44 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ACTKCTQRYPFEELSQGQQLCKECRIAHPI-VKCTYCRSEFQQEXXXXXXXXXXXXXXXXXXXPKPCQYC |
| ACTKCTQRYPFEELS.GQQLCKECRI.H.I.VKCTYCRSEFQQE...................PKP.QYC | |
| Retrocopy | ACTKCTQRYPFEELS*GQQLCKECRIVHQIIVKCTYCRSEFQQESKTNTICKKCAQNVKQFGTPKPYQYC |
| Parental | NIIAAFIGTKCQRCTNSEKKYGPPQTCEQCKQQCAFDRKEEGRRKVDGKLLCWLCTLSYKRVLQKTKEQR |
| NIIAAFIGTKCQRCTN.EKKYGPPQTCEQCKQ.CAFDRKEEGRRKVDGKLLCWL............K... | |
| Retrocopy | NIIAAFIGTKCQRCTNLEKKYGPPQTCEQCKQ*CAFDRKEEGRRKVDGKLLCWLYFI-IQESFTEDKRTE |
| Parental | KSLGSSHSNSSS-SSLTEKDQHHSKHHHHHHHHHHRHSSSHHKISNLSPEQEQGLWKQSHKSSATIQNET |
| ...G.SHSNSSS.SSLT.KDQH.SK............SSSHHKISNLSPEQEQGLWKQSHKSSATI.NET | |
| Retrocopy | EEPGMSHSNSSS>SSLTKKDQHQSKXXXXXXXXXXXXSSSHHKISNLSPEQEQGLWKQSHKSSATIENET |
| Parental | PKKKPKLS---PSGDSSSINQSADSGGTDNFVLISQLKEEVTSLKRLLQQRDQAILEKDKK |
| PKKKPKL......GDS.SINQSADSGGTD.FVLISQLKEEVTSLK.LLQQRDQAILEKDKK | |
| Retrocopy | PKKKPKLESKPSNGDSNSINQSADSGGTDSFVLISQLKEEVTSLKCLLQQRDQAILEKDKK |
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 |
|---|---|---|
| SRP017611_brain | 5 .96 RPM | 12 .73 RPM |
| SRP017611_kidney | 3 .75 RPM | 12 .38 RPM |
| SRP017611_liver | 0 .48 RPM | 3 .05 RPM |
Erinaceus europaeus was not studied using ChIP-Seq data.
Erinaceus europaeus was not studied using EST data.
Erinaceus europaeus was not studied using FANTOM5 data.
retro_eeur_195 was not experimentally validated.
Retrocopy orthology:
Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000008119 | 1 retrocopy |
retro_eeur_195 ,
|
| Oryctolagus cuniculus | ENSOCUG00000014549 | 1 retrocopy |