RetrogeneDB ID: retro_chof_1541

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_318185:360..916(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPC25
• Ensembl ID: ENSCHOG00000013303
• Aliases: None
• Description: SPC25, NDC80 kinetochore complex component [Source:HGNC Symbol;Acc:24031]

Sequence

>retro_chof_1541
CACAAGGACTCCATTAAAGCATTTGCAGAAAAGCTGTCTGTGAAGTTAAAGGAAGAAGACCGAATGGTTGAGATGTTTCT
GGAATATCAAAATCAGATCTGCCGGCAGAATAAGCTCATTCAGGAAAAAAAAGATAACTTGTTAAAGTTGATTGCTGAAG
TAAAACACAAAAAGCAAGAAATGGAAGTATTGACTGCAAATTTCTGGGATCATAAAGAAGAATAAGCAAAGAAGAAGGAA
ACTATTTCCACTGCTGACAAAGCTAATGAAGAGAGGTTGAAAAGGCTGCAGAAATCTGCAGACTTATATCAAGATTGACT
TGGACTAGAAATTCGAAAACTTTATGCTGATAAATTAGAGTTTATATTCACTAATATTGACCCTAAGCATCCTTAGATCC
ATATGTTTTCCTGCGCTGAATGAAGCAAGGGACTATGAAATGTCAGATAGTGCTCTGTATCTTGAACATCTAGCAGAATT
TCAAGAGAATATAAGGAAGACCAATAATTTTTCAGCTTTTCTTGCCAATGTTTGGAAAACTTTTACTTCTATGGTA

Alignment

ORF - retro_chof_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.66 %
• Parental protein coverage: 82.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YKDSIKAFAEKLSMKLKEEDRMVEMFLEYQNQICQQNQRIQEKKDNLLKLIAEVKCKKQEMEVLTANIQD
          .KDSIKAFAEKLS.KLKEEDRMVEMFLEYQNQIC.QN..IQ...DNLLKLIAEVK.KKQEMEVLTAN..D
Retrocopy HKDSIKAFAEKLSVKLKEEDRMVEMFLEYQNQICRQNKLIQXXXDNLLKLIAEVKHKKQEMEVLTANFWD

Parental  LKEEYAKKKETISTANKANEERLKRLQKSADLYKDRLGLEIRKIYGDKLQFIFTNIDPKHP-ENPYMFSL
          .KEE.AKKKETISTA.KANEERLKRLQKSADLY.D.LGLEIRK.Y.DKL.FIFTNIDPKHP...PY.F.L
Retrocopy HKEE*AKKKETISTADKANEERLKRLQKSADLYQD*LGLEIRKLYADKLEFIFTNIDPKHP<LDPYVF-L

Parental  R-LNEARDYEVSDSAPYLEHLAEFQENVRKTNNFSAFLANVRKTFTSMV
          R.LNEARDYE.SDSA.YLEHLAEFQEN.RKTNNFSAFLANV.KTFTSMV
Retrocopy R<LNEARDYEMSDSALYLEHLAEFQENIRKTNNFSAFLANVWKTFTSMV

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_1541 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013303	4 retrocopies	retro_chof_1070, retro_chof_1541 , retro_chof_2326, retro_chof_744,
Cavia porcellus	ENSCPOG00000005926	1 retrocopy	retro_cpor_1032,
Dasypus novemcinctus	ENSDNOG00000004429	1 retrocopy	retro_dnov_826,
Echinops telfairi	ENSETEG00000015642	1 retrocopy	retro_etel_1554,
Loxodonta africana	ENSLAFG00000004668	1 retrocopy	retro_lafr_497,
Monodelphis domestica	ENSMODG00000007753	1 retrocopy	retro_mdom_1828,
Tupaia belangeri	ENSTBEG00000012559	1 retrocopy	retro_tbel_2798,
Tursiops truncatus	ENSTTRG00000006112	1 retrocopy	retro_ttru_574,