RetrogeneDB ID: retro_chof_750

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_142833:2472..3260(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT75
• Ensembl ID: ENSCHOG00000003743
• Aliases: None
• Description: keratin 75 [Source:HGNC Symbol;Acc:24431]

Sequence

>retro_chof_750
GGCAGCAGCTTCTGGGGCAACCTGGGTGCCAGCATGGGTGTGATGGGGGGCTATGGAGGGACAGGGAATGCAGGGGGCAT
CATAGCCGACACGTTGAACCAGAGCCTGCTGAGCCCCCTTAAGCTGGAGGTGGACCCCAACATCCAGGCCATGCGGATGC
AGGAGAAGGAGCAGCAGATCAAGACCCTCAACAAGTTTGCCTCCTTCATCGACAAGGTGCGGTTCCTGGAGCAGCAGAAC
AAGAGGCTGGAGACCAAGTGGAACCTCCTGCAGCAGCAGAAGACTGCTGGGAGCAAAATGGACAACTTGTTCCAGAGCTA
CATCAACAACTTTCGGCGGCAGCAGGAGGCGCTGAGCCAGGAGAAGCTGAAGCTGGAGGCGGAGCTTGGCAACATGCGGG
GGCTGGTGGAAGACTTCAAGAGTAAGTACGAGGATGAGATCAACAAGCGAACAGAGATGGAGAATGAATTTGTCCTCATC
AGGAAGGATGTGGATGAAGCTTACATGAACAAAGTGGAGCTGGAGTCCCGCCTGGAAGGGCTGACTGATGTGATTAACTT
CCTCAGGCAGCTATATGAAGTGGACATGCGTGAGTTGCAGGCCCAGATCTCGGACACGTCCGTGGTCCTCTCCATGGACG
ACAGCCCTCCTTGGACCTGGACGGCATCATCGCTGAGGTCAAGGCCCAGTATGAGGACATCGCAAACTGCAGCTGGCCGA
GGCCGAGAGCATGTACCAGATCAGTACAAAGAGCTGCAACGCTGGCTGGGAAGCATGGGGATGACCTC

Alignment

ORF - retro_chof_750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.18 %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GSGVSSGFGYGGGAGGGFGSTGFPICSSGGIQEVTINQSLLTPLNLQIDPIIQQVRKEEWEQ-IKTLNNK
          GS......G...G..GG.G.TG......GGI...T.NQSLL.PL.L..DP.IQ..R..E.EQ.IKTLN.K
Retrocopy GSSFWGNLGASMGVMGGYGGTG----NAGGIIADTLNQSLLSPLKLEVDPNIQAMRMQEKEQQIKTLN-K

Parental  FASFIDKVRFLEEQNKVLETKWNLLQEQGSRTVRQNLESLFEAYLNGLRSQVENTTIKKDKLDTEMRKVQ
          FASFIDKVRFLE.QNK.LETKWNLLQ.Q...T.......LF..Y.N..R.Q.E.....K.KL..E.....
Retrocopy FASFIDKVRFLEQQNKRLETKWNLLQQQ--KTAGSKMDNLFQSYINNFRRQQEALSQEKLKLEAELGNMR

Parental  DIMEDVKVRYEDEINRHTAAENELVALKKDVDASCMNKVELEAKFNALTEEISFFHMLYETELSHMQTQV
          ...ED.K..YEDEIN..T..ENE.V...KDVD...MNKVELE.....LT..I.F...LYE......Q.Q.
Retrocopy GLVEDFKSKYEDEINKRTEMENEFVLIRKDVDEAYMNKVELESRLEGLTDVINFLRQLYEVDMRELQAQI

Parental  SDTSVVLSMDNN-RCLDLDSIIAEVKAQYKDIAQRS-RAEAESWYQ-TKYEELQ-VTAGRHSNDL
          SDTSVVLSMD.....LDLD.IIAEVKAQY.DIA..S..AEAES.YQ...Y.ELQ...AG.H..DL
Retrocopy SDTSVVLSMDDS<PSLDLDGIIAEVKAQYEDIANCS<LAEAESMYQ<DQYKELQ<TLAGKHGDDL

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_750 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 4 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003743	10 retrocopies	retro_chof_1530, retro_chof_1645, retro_chof_2414, retro_chof_2471, retro_chof_2544, retro_chof_2704, retro_chof_322, retro_chof_693, retro_chof_750 , retro_chof_915,
Choloepus hoffmanni	ENSCHOG00000011913	4 retrocopies	retro_chof_1848, retro_chof_2381, retro_chof_2385, retro_chof_778,
Microcebus murinus	ENSMICG00000002186	1 retrocopy	retro_mmur_747,
Nomascus leucogenys	ENSNLEG00000017753	1 retrocopy	retro_nleu_1726,