RetrogeneDB ID: retro_chof_2704

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_9918:20198..21348(-)
• 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_2704
AGCCGCTCTTACACGAGCGGGCCCGGCACCCGCGTCAGCTCCTACTCTCGGGTGGGCAGCGGTGGCAGCAACTTCCGGGG
CAACCTGGGCGCTGGCATGGGTCTGATGGGGGGCTATGCAGGGGCAGGGAGTGCCGGGGGTATCACAGCCGTCACGTTGA
ACCAGAGCCTGCTGAGCCCCCTTAAGCTGGAGGTGGACCCCAACATCCAGGCCGTGCGGATGCAGGAGAAGGAGCAGATC
AAGTCCCTGAACAACAAGTTTGCTTCCTTCATCGACAAGGTGCGGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAA
GTGGAGCCTTCTGCAGCAGCAGAAGACTGCTGGGAGCAAAATGGACAACTTGTTCGAGAGCTACATCAACAACCTTCGGC
GGCAGCACGAGGCGCTGAGCCAGGAGAAGCTGAAGCTGGAGGCGGAGCTTGGCAACATGCAGGGGCTGGTGGAAGACTTC
AAGAATAAGTACGAGGATGAGACCAACAAGCGAACAGAGATGGAGAATGAATTTGTCCTCATCAAGAAGGATGTGGATGA
AGCTTACATGAACAAAGTGGAGCTGGAGTCCCGCCTGGAAGGGCTGACCGATGAGATTAACTTCCTCAGGCAGCTATATG
AAGCGGAGATCCGTGAGCTGCAGGCCCAGATCTTGGACACGTCTGTGGTCCTCTCCATGGACAACAGCCGCTCCCTGGAC
CTGGATGGCATCATGGCCGAGGTCAAGGCCCAGTATGAGGACATCGCCAACCGCAGCCGGGCAGAAGCCGAGAGCATGTA
CCAGATCAATACGAGGAGCTGCAGACACTGGCCGGGAAGCATGGGGATGACCCCCGCCGCACAAAGACAGAGATCTCTGA
GATGAACCAGACCATCAGCCGGCTCCAGGCTGAGACCAAGGGCCTGAAGAGCCAGAGGGCTTCCCTGGAGGCCGGCATTG
CTGATGCCGAGCAGCATGGGGAGCTGGCCATTAGGGATGCCAATGCCAAGTTGGCCCAGCTGGAGGCCGCCCTACACCAG
GCCAAGCAGGACATGGCGCAGCAGCTGCACAAGTACCAGGAGCTGATGAACGTCAGCTGGCCCTGGACACTGAGATCACC
ACCTACTGCAAGCTGCTGGAGGATGAGGAG

Alignment

ORF - retro_chof_2704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 80.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSNFQSGFGSRASNGFGFGSGVSS---GFGYGGGAGGGFGSTGFPICSSGGIQEVTINQSLLTPLNLQID
          S....SG.G.R.S.....GSG.S......G.G.G..GG....G....S.GGI..VT.NQSLL.PL.L..D
Retrocopy SRSYTSGPGTRVSSYSRVGSGGSNFRGNLGAGMGLMGGYAGAG----SAGGITAVTLNQSLLSPLKLEVD

Parental  PIIQQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQGSRTVRQNLESLFEAYLNGLRS
          P.IQ.VR..E.EQIK.LNNKFASFIDKVRFLE.QNK.LETKW.LLQ.Q...T.......LFE.Y.N.LR.
Retrocopy PNIQAVRMQEKEQIKSLNNKFASFIDKVRFLEQQNKMLETKWSLLQQQ--KTAGSKMDNLFESYINNLRR

Parental  QVENTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELVALKKDVDASCMNKVELEAKFNALTE
          Q.E.....K.KL..E....Q...ED.K..YEDE.N..T..ENE.V..KKDVD...MNKVELE.....LT.
Retrocopy QHEALSQEKLKLEAELGNMQGLVEDFKNKYEDETNKRTEMENEFVLIKKDVDEAYMNKVELESRLEGLTD

Parental  EISFFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAEVKAQYKDIAQRSRAEAESWYQ-TKYEE
          EI.F...LYE.E....Q.Q..DTSVVLSMDN.R.LDLD.I.AEVKAQY.DIA.RSRAEAES.YQ...YEE
Retrocopy EINFLRQLYEAEIRELQAQILDTSVVLSMDNSRSLDLDGIMAEVKAQYEDIANRSRAEAESMYQ<DQYEE

Parental  LQVTAGRHSNDLHNTKHEISEMNRTIQTLRAEIGSIKKQCSNLQTAITDAEQCGELALKDARAKLVGLEE
          LQ..AG.H..D...TK.EISEMN.TI..L.AE....K.Q...L...I.DAEQ.GELA..DA.AKL..LE.
Retrocopy LQTLAGKHGDDPRRTKTEISEMNQTISRLQAETKGLKSQRASLEAGIADAEQHGELAIRDANAKLAQLEA

Parental  ALQKAKQDMACLLHEYQELMTI-KLALEVEIVTH-KLLEGEE
          AL..AKQDMA..LH.YQELM....LAL..EI.T..KLLE.EE
Retrocopy ALHQAKQDMAQQLHKYQELMNV<QLALDTEITTYCKLLEDEE

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_2704 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,