RetrogeneDB ID: retro_chof_1823

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_39455:8549..9610(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HOMER1
• Ensembl ID: ENSCHOG00000013410
• Aliases: None
• Description: homer homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:17512]

Sequence

>retro_chof_1823
CAGAAACTTCAGAGCAAGTTTTCACTGGGCAAAATGGGGGAACAACCCATTTTCAGCACTCGAGCTCATGTCTTCCAGAT
TGACCCAAACACACAGAAGAACTGGGTACCCACCAGCAAGCACGCAGTTACTGAGTCTTATTTCTATAACAGCACAAGAA
ATGTGTATAGGATAATCAGTTTAGATGGCTCAAAGGCAATAATAAGCAGCACCATCACCCTAAACATGACATTTACTAAA
ACATTTCAGAAGTTTAGCCAGTGGGCTGATAGCCGGGCCAATACTGTTTATGGACTGGGATTCTCCTTTGAGCATCATCT
CTCAAAATTTGCAGAAAAGTTTTAGGCATTAAAGAAGCTGCTCGACTAGCAAAGGAAAAATCACAAGAAAAAATGGAACT
TACCAGTACGCTTTCACAGGAATCAACAGGAGGGGATCTTCAGTCTCTAAGTCCAGAAAGTATCAGTGGGACAGACGATG
AAAGAATGCCTGACATGACTCAGAACTCAGAGCCAAGGGTTGAACCAACCCAGAATGCATTGCCCTTTTCACATAGTTTC
AGTGATCAGCAAACATTGGGAGGCTGAACTGGCTACCCTCAAAGGAAATAATGCCCAACTCACTGCAGCCCCATTGGAGT
CCACTGCCAATGTGAAACAATGGAAACAGCAGCTTGCTGCATATCAAGAGGAAGCAGAACATCTACACAAGCGGGTGACT
AAGCTTGAATGTGTTAGTAGCCAAGCAAATGCTGTGCATACCCATAAGACAGAATTAAATGAGACAATACAAGAATTAGA
AGAGACACTGAAAGTGAAGGAAGAGGAAGTAGAAAGATTAAAACAAGAAATTGATAATGCCAGAGAACTATAGGAACAAG
GGGCCTCTTTGACTCAGAAGCTACAGGAAGTAGAAATTCTGAACAAAGACCTGGAAGGACAACTGTCTGCTTAAAGTGAT
GTCTGGAGAAAAGTCAGAATGAGCAAGAAGCTTTTTGCAATAACCTGAAGACACTTTTAGAAATTCTTGATGGAAAAATA
TTTGAACTAACAGAATTACGA

Alignment

ORF - retro_chof_1823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.71 %
• Parental protein coverage: 97.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKLKSKFSLGKMEEQPIFSTRAHVFQIDPNTKKNWVPTSKHAVTVSYFYDSTRNVYRIISLDGSKAIINS
          .KL.SKFSLGKM.EQPIFSTRAHVFQIDPNT.KNWVPTSKHAVT.SYFY.STRNVYRIISLDGSKAII.S
Retrocopy QKLQSKFSLGKMGEQPIFSTRAHVFQIDPNTQKNWVPTSKHAVTESYFYNSTRNVYRIISLDGSKAIISS

Parental  TITPNMTFTKTSQKFGQWADSRANTVYGLGFSSEHHLSKFAEKF-QEFKEAARLAKEKSQEKMELTSTPS
          TIT.NMTFTKT.QKF.QWADSRANTVYGLGFS.EHHLSKFAEKF....KEAARLAKEKSQEKMELTST.S
Retrocopy TITLNMTFTKTFQKFSQWADSRANTVYGLGFSFEHHLSKFAEKF<LGIKEAARLAKEKSQEKMELTSTLS

Parental  QESAGGDLQSPLTPESINGTDDERTPDVTQNSEPRVEPTQNALPFSHS-SVISKHWEAELATLKGNNAKL
          QES.GGDLQS.L.PESI.GTDDER.PD.TQNSEPRVEPTQNALPFSHS.SVISKHWEAELATLKGNNA.L
Retrocopy QESTGGDLQS-LSPESISGTDDERMPDMTQNSEPRVEPTQNALPFSHS>SVISKHWEAELATLKGNNAQL

Parental  TAALLESTANVKQWKQQLAAYQEEAERLHKRVTELECVSSQANAVHTHKTELNQTIQELEETLKVKEEEI
          TAA.LESTANVKQWKQQLAAYQEEAE.LHKRVT.LECVSSQANAVHTHKTELN.TIQELEETLKVKEEE.
Retrocopy TAAPLESTANVKQWKQQLAAYQEEAEHLHKRVTKLECVSSQANAVHTHKTELNETIQELEETLKVKEEEV

Parental  EGEFHHIDNARELQEQRDSLTQKLQEVEIRNKDLEGQLSD-LEQRLEKSQNEQEAFRNNLKTLLEILDGK
          E.....IDNAREL.EQ..SLTQKLQEVEI.NKDLEGQLS..L...LEKSQNEQEAF.NNLKTLLEILDGK
Retrocopy ERLKQEIDNAREL*EQGASLTQKLQEVEILNKDLEGQLSA<LK*CLEKSQNEQEAFCNNLKTLLEILDGK

Parental  IFELTELR
          IFELTELR
Retrocopy IFELTELR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1823 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013410	1 retrocopy	retro_chof_1823 ,