RetrogeneDB ID: | retro_chof_1873 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_41046:2853..5321(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCHOG00000001946 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HSPH1 | ||
| Ensembl ID: | ENSCHOG00000013998 | ||
| Aliases: | None | ||
| Description: | heat shock 105kDa/110kDa protein 1 [Source:HGNC Symbol;Acc:16969] |
Retrocopy-Parental alignment summary:
>retro_chof_1873
TCAGTCATATCATTTGGATCAAAAAACAGAACAATTGGAGTTGCAGCAAAAAATCAGCAAATCACTCATGCAAACAACAC
AGTATCTAACTTCAAGAGATTTCATGGCCGAGCATTCAGTGACCCCTTCATTCAAAAAGAGAAGGAAAACTTAAGCTACG
ATTTGGTTCCGATGAAAAATGGTGGAGTTGGAATAAAGGTAATGTACATGGATGAAGAACATCTGTTTAGTGTGGAACAG
ATAACAGCCATGTTGTTGACTAAGTTAAAGGAAACTGCTGAAAACAACCTCAAGAAGCCAGTGACAGATTGTGTTATTTC
AGTGCCCTCCTTCTTCACGGATGCGGAGAGGCGATCTGTGTTGGATGCTGCACAGATTGTTGGCCTAAACTGCTTGAGAC
TTATGAATGACATGACTGCTGTTGCTTTGAATTATGGAATTTATAAGCAGGATCTCCCCGGCCTGGATGAGAAACCTCGG
ATAGTGGTTTTTGTTGATATGGGACATTCAGCTTTTCAAGTGTCTGCCTGTGCCTTTAACAAGGGAAAATTGAAGGTATT
GGGAACTGCTTTTGATCCTTTCTTGGGAGGAAAGAACTTTGATGAAAAGTTAGTGGAACATTTTTGTGCAGAATTTAAGA
CCAAGTACAAGTTGGATGCAAAATCCAAAATTCGAGCACTCCTTCGTCTGTATCAGGAGTGTGAAAAGTTGAAAAAGCTA
ATGAGCTCGAACAGCACAGACCTGCCATTGAATATCGAGTGCTTTATGAATGACAAAGATGTTTCGGGAAAGATGAACAG
GTCACAATTTGAAGAACTCTGTGCTGACCTGCTGCAAAAAATAGAAATACCCCTTTATTCGCTGATGGAACAAACTCGAC
TAAAAGTAGAAGATGTGAGTGCTGTTGAGATCGTTGGAGGCACTACACGAATTCCAGCTGTGAAAGAAAGAATTGCCAAG
TTCTTCGGAAAAGACATCAGCACAACCCTTAACGCAGATGAAGCCGTAGCCAGAGGATGTGCGCTGCAGTGTGCAGCTCT
TTCCCCGGCTTTTAAAGTTAGGGAGTTTTCTGTCACAGATGCAATTCCTTTTCCGATATCGCTGATCTGGAATCACGATT
CAGAAGATACTGAAGGTGTTCATGAAGTGTTCAGCCGCAACCATGCTGCACCTTTCTCCAAAGTTCTCACCTTCTACAGA
AGGGGGCCTTTTGAGCTAGAAGCTTTCTATTCTGATCCTCAAGGAGTTCCATATCCAGAAGCAAAAATAGGCTGCTTCAT
AGTTCAGAATGTTTCTGCCCAGAAAGATGGAGAAAAATCTAAGGTGAAAGTTAAAGTGCGGGTCAACACCCATGGCATTT
TCACCATCTCTACAGCATCTATGGTGGAGAAGATCCCAACTGAGGAAAATGAAGGGTCATCTCTTGAAGCAGACATGGAG
TGTGCTAATCAGAGACCACCAGAAAACCCCGACAGTGATAAAAATATCCAGCAAGACAACAGTGAAGCTGGAACACAGCC
CCAGGTACAAACTGATGCTCAACAAACCTCACAGTCTCCCCCTTCATCTGAACTTACCTCAGAAGAAAACAAAATCCCAG
ATGCTGACAAAGCCAATGAAAAGAAGGTTGACCAGCCTCCAGAAGCTAAAAAACCCAAAATAAAGGTGGTGAACGTTGAG
CTGCCTATTGAAGCCAATTTGGTCTGGCAGTTAGGGAAAGACCTTCTTAACATGTATATTGAGACAGAGGGTAAGATGAT
AATGCAGGATAAATTGGAAAAGGAAAGAAATGACGCTAAAAATGCGGTGGAAGAGTATGTGTATGAGTTCAGGGACAAGC
TCTGTGGACCATATGAAAAATTCATAAGTGAACAGGATCCTCAGCATTTCCTGAGGCTCTTCTCTTTTTCTGAAGACTGG
CTCTATGAAGAAGGAGAGGACCAAGCCAAACAGGCATATGTGACAAGCTGGAAGAGTTAACGAAAATTGGCACTCCAATT
AAAATCCGGTTTCAAGAGGCTGAGGACCGGCCAAAACTGTTTGAAGAGCTGGGGCAGAGGCTCCAGCACTACGCCAAGAT
AGCAGCTGACTTCAGAAACCAGGATGAGAAGTATAACCATATCGATGAGTCTGAAATGAAGAAGGTTGAGAAGTCTGTCA
ATGAAGTGATGGAGTGGATGAACAACATCATAAATGTGCAGGCTAAAAGGAGCCTGGAGCAGGACCCTGTTGTCCAAGCA
CAGGAAATTAAAGCAAAATTGAAGGAACTGAACAACACTTGTGAACCAATTGTAACACAACCCAAGCCAAAAATCGAGTC
ACCCAAACTGGAGAGAACTCCAAATGGCCCAAATGTTGATAAGAAGGAAGAAGATTTAGAAGGCAAGAATGATTTTGGTG
CTGAGCCGCCACATCAGAATGGTGACTGCTACCCAAACGAGAAGAACTCCGCCCACATGGACTTGGAC
ORF - retro_chof_1873 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.69 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFSDPFIQKEKENLSYDLVPMKNGGVGIKVMYM |
| SVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFSDPFIQKEKENLSYDLVPMKNGGVGIKVMYM | |
| Retrocopy | SVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFSDPFIQKEKENLSYDLVPMKNGGVGIKVMYM |
| Parental | DEEHLFSVEQITAMLLTKLKETAENNLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTA |
| DEEHLFSVEQITAMLLTKLKETAENNLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTA | |
| Retrocopy | DEEHLFSVEQITAMLLTKLKETAENNLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTA |
| Parental | VALNYGIYKQDLPGLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCA |
| VALNYGIYKQDLPGLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCA | |
| Retrocopy | VALNYGIYKQDLPGLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCA |
| Parental | EFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCADLLQK |
| EFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCADLLQK | |
| Retrocopy | EFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCADLLQK |
| Parental | IEIPLYSLMEQTRLKVEDVSAVEIVGGTTRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAALSPA |
| IEIPLYSLMEQTRLKVEDVSAVEIVGGTTRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAALSPA | |
| Retrocopy | IEIPLYSLMEQTRLKVEDVSAVEIVGGTTRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAALSPA |
| Parental | FKVREFSVTDAIPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFYRRGPFELEAFYSDPQGVPYPE |
| FKVREFSVTDAIPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFYRRGPFELEAFYSDPQGVPYPE | |
| Retrocopy | FKVREFSVTDAIPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFYRRGPFELEAFYSDPQGVPYPE |
| Parental | AKIGRFIVQNVSAQKDGEKSKVKVKVRVNTHGIFTISTASMVEKIPTEENEGSSLEADMECANQRPPENP |
| AKIG.FIVQNVSAQKDGEKSKVKVKVRVNTHGIFTISTASMVEKIPTEENEGSSLEADMECANQRPPENP | |
| Retrocopy | AKIGCFIVQNVSAQKDGEKSKVKVKVRVNTHGIFTISTASMVEKIPTEENEGSSLEADMECANQRPPENP |
| Parental | DSDKNIQQDNSEAGTQPQVQTDAQQTSQSPPSSELTSEENKIPDADKANEKKVDQPPEAKKPKIKVVNVE |
| DSDKNIQQDNSEAGTQPQVQTDAQQTSQSPPSSELTSEENKIPDADKANEKKVDQPPEAKKPKIKVVNVE | |
| Retrocopy | DSDKNIQQDNSEAGTQPQVQTDAQQTSQSPPSSELTSEENKIPDADKANEKKVDQPPEAKKPKIKVVNVE |
| Parental | LPIEANLVWQLGKDLLNMYIETEGKMIMQDKLEKERNDAKNAVEEYVYEFRDKLCGPYEKFISEQDHQHF |
| LPIEANLVWQLGKDLLNMYIETEGKMIMQDKLEKERNDAKNAVEEYVYEFRDKLCGPYEKFISEQD.QHF | |
| Retrocopy | LPIEANLVWQLGKDLLNMYIETEGKMIMQDKLEKERNDAKNAVEEYVYEFRDKLCGPYEKFISEQDPQHF |
| Parental | LRLLTETEDWLYEEGEDQAKQAYV-DKLEELTKIGTPIKIRFQEAEDRPKLFEELGQRLQHYAKIAADFR |
| LRL....EDWLYEEGEDQAKQAYV.DKLEELTKIGTPIKIRFQEAEDRPKLFEELGQRLQHYAKIAADFR | |
| Retrocopy | LRLFSFSEDWLYEEGEDQAKQAYV<DKLEELTKIGTPIKIRFQEAEDRPKLFEELGQRLQHYAKIAADFR |
| Parental | NQDEKYNHIDESEMKKVEKSVNEVMEWMNNIINVQAKRSLEQDPVVQAQEIKAKLKELNNTCEPIVTQPK |
| NQDEKYNHIDESEMKKVEKSVNEVMEWMNNIINVQAKRSLEQDPVVQAQEIKAKLKELNNTCEPIVTQPK | |
| Retrocopy | NQDEKYNHIDESEMKKVEKSVNEVMEWMNNIINVQAKRSLEQDPVVQAQEIKAKLKELNNTCEPIVTQPK |
| Parental | PKIESPKLERTPNGPNVDKKEEDLEGKNDFGAEPPHQNGDCYPNEKNSAHMDLD |
| PKIESPKLERTPNGPNVD............GAEPPHQNGDCYPNEKNSAHMDLD | |
| Retrocopy | PKIESPKLERTPNGPNVDXXXXXXXXXXXXGAEPPHQNGDCYPNEKNSAHMDLD |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_1873 was not experimentally validated.
Retrocopy orthology:
Choloepus hoffmanni 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000004852 | 1 retrocopy | |
| Choloepus hoffmanni | ENSCHOG00000013998 | 1 retrocopy |
retro_chof_1873 ,
|
| Monodelphis domestica | ENSMODG00000009347 | 1 retrocopy |