RetrogeneDB ID: | retro_chof_534 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_119175:1..1912(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIM33 | ||
| Ensembl ID: | ENSCHOG00000001716 | ||
| Aliases: | None | ||
| Description: | tripartite motif containing 33 [Source:HGNC Symbol;Acc:16290] |
Retrocopy-Parental alignment summary:
>retro_chof_534
CCAGTATGCCGCCAGGAATGCAGACAGATAGACTTTGTGAATAATTTATTTTGTGAAAGTCACATCTGAAGCTCCCAGCA
GTTCTGATGAGAAGTCAGAACAGGTATGTACTAGTTGTGAAGACAATGCAAGTGCAGTTGGCTTTTGTGTAGAATGTGGA
GAGTGGCTGTGTAAGACATGTATAGAAGCACATCAAAGAGTAAAATTCACTAAAGATCACCTGATCAGGAAGAAAGAAGG
TGTCTGAGAGTCTGTTGGAGCATCTGATCAACGCCCTGTTTTCTGCCCTGTACACAAACAAGAACAGTTGAAACTTTTCT
GTGAAACATGTGATAGATTCACATGTAGAGACTGCCAGCTATTGGAACACAAAGAACATAGGTATCAGTTTTTGAAAGAA
GCGTTTCAAAATCAGAAAGGTGCGATTGAAAACCTACTGGCTAAGCTTCTAGAGAAGAAAAATTATGTTCATTTTGCAGC
TACTCAGGTGCAGAATAGGATAAAAGAAGTAAATGAGACTTACAAACGAGTAGAACAGGAAATAAAAGTGGCCATTTTCA
CCCTTATCAATGAAATTAATAAGAAAGGAAAATCTCTCTTACAGCAGCTAGAGAATGTCACAAAAGAAAGACAGATGAAG
TTAATACAGCAGCAGAATGACCTCACAGGCCTTTCCCGACAGGTGAAGCATGTTATGAACTTTACAAACTGGGCAACTGC
AAGTGGCAGCAGCACAGCACTACTGTATAGCAAGCGACTGATTACTTTTCAGTTGTGTCATATTTTGAAAGCACGGTGTG
ATCCTGTCCCTGCTGCTAATGGAGCAATACGTTTCCATTGTGATCCTACTTTCTGGGCAAAGAATGTAGTCAATTTAGGT
AATCTAATAATAGAGAGTAAACCAGCTCCTGGTTATACTCCTAATGTTGTAGTTGCGCAAGTTCCTCCAGGGACAAACCA
CATTAGTAAAACCCCTGGACAGATTAATTTAGCACAGCTTCGACTCCAGCACATGCAGCAACAGCTTTATGCACAGAAAC
ATCAGCAGTTGCAACAGATGAGGATGCAGCAACCACCAGCACCTGTACCAACAACAACAGCAAGAACACAACAACATCCT
AGACAAGCAGCCCCTCAGATGTTACAACAACAGCCTCCAAGATTGATCAGTGTGCAAACAATGCAAAGAGGCCAATATGA
ATTGTGGAGCTTTCCAAGCCCATCAGATGAGAATGGCTCAGAATGCTGCCCAAATACCAGGGATACCCAGGCACAGCGGC
CCTCAGTATTCCATGATGCAGCCACACCTCCAAAGACAACACTCAAACCCAGGGCATTCTGGACCCTTTCCTGTTGTATC
AGTGCACAATAACACAATCAACCCAACCAGCCCTACTACAGCTACTATGGCAAATGCGAACAGAGGTCCCACCAGCCCAT
CTGTTACAGCAATAGAGCTTATCCCTTCAGTTACCAATCCAGAAAACCTTCCATCACTGCCAGATATTCCACCCATACAG
TTGGAAGATGCTGGTTCAAGTAGTTTAGATAATCTACTAAGTAGATATATCTCAGGCAGTCACCTACCCCCACAGCCTAC
AAGCACCATGAATCCTTCCCCAGACCCTCTGCCCTATCTCCAGGATCATCAGGTTTATCCAATTCCCACACACCTGTGAG
ACCCCCAGTACTTCTAGTACTGGCAGTCGAGGAAGCTGTGGGTCATCAGGAAGAACAGCTGAGAAGACAAGTCTTAGTTT
CAAAACTGATCAAGTGAAAGTCAAGCAAGAACCTGGGACTGAAGATGAAATATGTAGTTTTTCAGGAGCTGTGAAACAAG
AAAAGACAGAGGATGGCAGGAAGAGTGCCTGCATGTTGAGCAGTCCTGAGAGTAGCTTGATACCACCTCTC
ORF - retro_chof_534 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.29 % |
| Parental protein coverage: | 67.05 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | PVCRQECRQIDLVDN-YFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKF |
| PVCRQECRQID.V.N.YFVK.TSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKF | |
| Retrocopy | PVCRQECRQIDFVNN>YFVKVTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKF |
| Parental | TKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK |
| TKDHLIRKKE.V.ESVGAS.QRPVFCPVHKQEQLKLFCETCDR.TCRDCQLLEHKEHRYQFL.EAFQNQK | |
| Retrocopy | TKDHLIRKKEGV*ESVGASDQRPVFCPVHKQEQLKLFCETCDRFTCRDCQLLEHKEHRYQFLKEAFQNQK |
| Parental | GAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKE |
| GAIENLLAKLLEKKNYVHFAATQVQNRIKEVNET.KRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKE | |
| Retrocopy | GAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETYKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKE |
| Parental | RQMKLIQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFH |
| RQMKLIQQQND.TGLSRQVKHVMNFTNWA.ASGSSTALLYSKRLITFQL.HILKARCDPVPAANGAIRFH | |
| Retrocopy | RQMKLIQQQNDLTGLSRQVKHVMNFTNWATASGSSTALLYSKRLITFQLCHILKARCDPVPAANGAIRFH |
| Parental | CDPTFWAKNVVNLXXXXXXXXXXXXXXXXVVVAQVPPGTNHIRKTPGQINLAQLRLQHMQQQVYAQKHQQ |
| CDPTFWAKNVVNL................VVVAQVPPGTNHI.KTPGQINLAQLRLQHMQQQ.YAQKHQQ | |
| Retrocopy | CDPTFWAKNVVNLGNLIIESKPAPGYTPNVVVAQVPPGTNHISKTPGQINLAQLRLQHMQQQLYAQKHQQ |
| Parental | LQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRG-NMNCGAFQAHQMRMAQNAARI |
| LQQMRMQQPPAPVPTTT..TQQHPRQAAPQMLQQQPPRLISVQTMQRG.NMNCGAFQAHQMRMAQNAA.I | |
| Retrocopy | LQQMRMQQPPAPVPTTTARTQQHPRQAAPQMLQQQPPRLISVQTMQRG>NMNCGAFQAHQMRMAQNAAQI |
| Parental | PGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNNTINPTSPTTATMANANRGPTSPSVTAIELIP |
| PGIPRHSGPQYSMMQPHLQRQHSNPGH.GPFPVVSVHNNTINPTSPTTATMANANRGPTSPSVTAIELIP | |
| Retrocopy | PGIPRHSGPQYSMMQPHLQRQHSNPGHSGPFPVVSVHNNTINPTSPTTATMANANRGPTSPSVTAIELIP |
| Parental | SVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPG-PSALSPGSSGLSNSHT |
| SVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSP..PSALSPGSSGLSNSHT | |
| Retrocopy | SVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPD<PSALSPGSSGLSNSHT |
| Parental | PVRP-PSTSSTGSRGSCGSSGRSAEKTSLSFKSDQVKVKQEPGTEDEICSFSGAVKQEKTEDGRRSACML |
| PVRP.PSTSSTGSRGSCGSSGR.AEKTSLSFK.DQVKVKQEPGTEDEICSFSGAVKQEKTEDGR.SACML | |
| Retrocopy | PVRP<PSTSSTGSRGSCGSSGRTAEKTSLSFKTDQVKVKQEPGTEDEICSFSGAVKQEKTEDGRKSACML |
| Parental | SSPESSLTPPL |
| SSPESSL.PPL | |
| Retrocopy | SSPESSLIPPL |
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_534 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000001716 | 1 retrocopy |
retro_chof_534 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000024757 | 1 retrocopy |