RetrogeneDB ID: | retro_chof_697 | ||
Retrocopy location | Organism: | Sloth (Choloepus hoffmanni) | |
| Coordinates: | scaffold_136553:4158..4901(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TFCP2L1 | ||
| Ensembl ID: | ENSCHOG00000000115 | ||
| Aliases: | None | ||
| Description: | transcription factor CP2-like 1 [Source:HGNC Symbol;Acc:17925] |
Retrocopy-Parental alignment summary:
>retro_chof_697
CTCTTCCAGCACAGGCAGCCTGAGCTTGACAATCAGCACAACTCCAGCACCTATCTGCGCCATGTCCTCGCTCTGCCCAT
CTTCAAGCGGGAGGAGCCCCAGCTGTCCCCTGAGAACGAGGCCCACCTGCAGCCCTTGCAGTATGTGCTGTGTGCCCCGA
CGTCCCCTGGACGAAGAGATGCTGACCTACCTCAACCAAGGTCAGTCTTATGAAATCCAACTCCTGGAGAATCGAAGGTG
GGAGATTTTCTAGATCTGAACACAAAATATGTCAAGAACATCATCTGCATGGTTTTCCATGACCATCGGCTGCAGTATAT
GGAGCACCAGCAGCTGGAGGGCTGGAGGTGGAGCCGGCCTGGAGACCGGATCCTGGACCTTGGTATTCTACTGTCTGTTG
GTATCTTGGACCCCAGGACCAGCCGAACCCAGTTGAACACTGTCAAGTTTTTGTGGGACCCTTCGAAGAGAGCCTCTGCC
TTCCTTCAGATGCACGGCACATCAGCAAGGAATTCACCCTGAGGAAGCACGCGGGCTAGAAGGGGGTGACTTTCCGCGTG
CAGATCGATAAGCAGAAGGCGATTGATTACCTGCACTCTGCCAGCTGCCTGGTGAAGGTGTTCAAGCCAAAGGGAGCCAA
CCGGAAGCAGAAGACTGACTAGGAGAAGAAGGAGAAAAGAACTGCCCAAGAGAAGATGTACCAGCTGTCCTACAAGACCA
CTGTCCTCATGGAGTGCTCTCCA
ORF - retro_chof_697 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.51 % |
| Parental protein coverage: | 57.96 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LFRQRQSEQNIQHKSGSYLPDVLALPIFKQEEPQLSPE-EARLPPLQYVLCATF-PELQEETPDLNK-QS |
| LF..RQ.E...QH.S..YL..VLALPIFK.EEPQLSPE.EA.L.PLQYVLCA...P...E....LN..QS | |
| Retrocopy | LFQHRQPELDNQHNSSTYLRHVLALPIFKREEPQLSPENEAHLQPLQYVLCAPT>PLDEEMLTYLNQGQS |
| Parental | YEIRLLENR-KLGDFQDVNTKXXXRV---VFRDCRLQSTEHQQREGWRWS-GGDRVPGTDSAPSVGMLDH |
| YEI.LLENR.K.GDF.D.NTK........VF.D.RLQ..EHQQ.EGWRWS..GDR........SVG.LD. | |
| Retrocopy | YEIQLLENR<KVGDFLDLNTKYVKNIICMVFHDHRLQYMEHQQLEGWRWSRPGDRILDLGILLSVGILDP |
| Parental | SASPIQLNTIGFRWGPSKRASAFSKVHCISTEFTP-RKQGGKRG-VPFRVQIDRFKSKSREYMDHLYSSC |
| ..S..QLNT..F.W.PSKRASAF...H..S....P.......RG.V.FRVQID..K.K...Y......SC | |
| Retrocopy | RTSRTQLNTVKFLWDPSKRASAFLQMHGTSARNSP*GSTRARRG<VTFRVQID--KQKAIDYLHS--ASC |
| Parental | HIKVFQPKGGDQKQRSAGEGMEKRTAQEKKCP-SYETTILTEGPP |
| ..KVF.PKG...KQ....E..EKRTAQEK....SY.TT.L.E..P | |
| Retrocopy | LVKVFKPKGANRKQKTD*EKKEKRTAQEKMYQLSYKTTVLMECSP |
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_697 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000000115 | 1 retrocopy |
retro_chof_697 ,
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