RetrogeneDB ID: retro_chof_1645

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_350029:8..1167(-)
• 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_1645
AGCCGTTCTTACACCAGTGGGCCTGGCACCCACGTCAGCTCCTACTCTCAGGTGGGCAGCGGCAACAGCAGCTTCCAGGG
CAACCTGGGCACCAGCATGGGTCTGATGGAGGGCTATGGAGGGGCAGAGAGTGCAGGGGGCATCACAGCCATCACGTTGA
ACCAGAGCCTGCTGAGCCCCCTTAAGCTGGAGGTGGACCCCAACATCCAGGCTGCTCGGATGCAGAAGGAGCCGATCAAG
ACCCTCAACAACAAGTTTGCTTCCTTCATCAACAAGGTGCGGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTG
TAGTCTCCTGCAGTAGCAGAAGACTGCTGGGAGCAAAATGGACAATTTGTTCGAGAGCTACATCAACAACCTTTGGCAGC
AGCACGAGGCGCTGAGCCAGTAGAAGCTGAAGCTGGAGGCAGAGCTTGGCAACATGCAGGGGCTGGTGGAAGACTTCAAG
AATGAGTACGAGGATGAGATCAACAAGCGAACAGAGATGGAGAATGAATTTGTCCTCATCAAGAAGGATGTGGATGAAGC
TTACATGAACAAAGTAGAGCTGGAGACCCGCCTGGGAGGGCTGACCGAAGAGATTAACTTCCTCAGGCAGCTATATGAAG
CGGAGATCCGTGAGCTGCAGGCCCAGATCTCTGACACGTCCGTGGTCCTCTCCATGGACAATAATCACTCCCTGGACCTG
GACAGCATCATCGCCGATGGTCAAGGCCCAGTATGAGGAGATCGCCAACCGCAGCCGGGCCGGGGCCAAGGGCATGTACC
AGATCAAGTACAAGGAGCTGCAAACACTGGCCGGGAAGCACAGGGATGACCTCCACGGCATGAAGACGGAGATCTCTGAG
ATGAACCAAACCATCAGCCGGCTCCAGGCTGAGATCAAGGGCCTGAAGGGCCAGAGGGCTTCCCTGGAGGCTGCCATTGT
GGATGCCAAGCAGCATGGGGAGCTGGCCAATAAGGACGCCAATGCCAAGTTGGCCCAGCCGGAAGCCACCCTGCACCACG
CCAAGCAGACATGGCACGGCAGCTGCACAAATAGCAGGAGCTGATGAACGTCAAGCTGGGCCCTGGACATTGAGATCGCC
ACCTACCACAAGCTGCTGGAGGGCAAGGAGAGCCAGCTG

Alignment

ORF - retro_chof_1645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.22 %
• Parental protein coverage: 81.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSNFQSGFGSRASNGFGFGSGVSSGFGYGGGAGGGFGSTGFPICSSGGIQEVTINQSLLTPLNLQIDPII
          S....SG.G...S.....GSG..S.F....G...G.........S.GGI...T.NQSLL.PL.L..DP.I
Retrocopy SRSYTSGPGTHVSSYSQVGSG-NSSFQGNLGTSMGLMEGYGGAESAGGITAITLNQSLLSPLKLEVDPNI

Parental  QQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQGSRTVRQNLESLFEAYLNGLRSQVE
          Q..R....E.IKTLNNKFASFI.KVRFLE.QNK.LETK..LLQ.Q...T.......LFE.Y.N.L..Q.E
Retrocopy QAARMQK-EPIKTLNNKFASFINKVRFLEQQNKMLETKCSLLQ*Q--KTAGSKMDNLFESYINNLWQQHE

Parental  NTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELVALKKDVDASCMNKVELEAKFNALTEEIS
          .....K.KL..E....Q...ED.K..YEDEIN..T..ENE.V..KKDVD...MNKVELE.....LTEEI.
Retrocopy ALSQ*KLKLEAELGNMQGLVEDFKNEYEDEINKRTEMENEFVLIKKDVDEAYMNKVELETRLGGLTEEIN

Parental  FFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAE-VKAQYKDIAQRSRAEAESWYQTKYEELQV
          F...LYE.E....Q.Q.SDTSVVLSMDNN..LDLDSIIA..VKAQY..IA.RSRA.A...YQ.KY.ELQ.
Retrocopy FLRQLYEAEIRELQAQISDTSVVLSMDNNHSLDLDSIIAD>VKAQYEEIANRSRAGAKGMYQIKYKELQT

Parental  TAGRHSNDLHNTKHEISEMNRTIQTLRAEIGSIKKQCSNLQTAITDAEQCGELALKDARAKLVGLEEALQ
          .AG.H..DLH..K.EISEMN.TI..L.AEI...K.Q...L..AI.DA.Q.GELA.KDA.AKL...E..L.
Retrocopy LAGKHRDDLHGMKTEISEMNQTISRLQAEIKGLKGQRASLEAAIVDAKQHGELANKDANAKLAQPEATLH

Parental  KAKQ-DMACLLHEYQELMTIKL-ALEVEIVT-HKLLEGEECRL
          .AKQ.DMA..LH..QELM..KL.AL..EI.T.HKLLEG.E..L
Retrocopy HAKQ<DMARQLHK*QELMNVKL>ALDIEIATYHKLLEGKESQL

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_1645 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,