RetrogeneDB ID: retro_chof_2471

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78406:5273..6412(+)
• 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_2471
TACACGAGCGGGTCCGGCACCTGCCTCAGCTCCTACTTTAGGGTGGGCAGCGGCGGCAGCAGCTTCCAGGGCAACCTGGG
TGCTGGCATGGGTCTGGTGGGGGGCTACAGAGGGGCAGGGAGTGCAGGGGGCATCACAACTGTCACGTTGAACCAGAGCC
TGCTGAGCCCCCTTAAGCTGGAGGTGGACCCCAACATCCAGGCTGTTCAGTTGCAAGAGAAGGAGCAGATCAAGACCCTC
AACTGCAAGTTTGCTTCCTTCATTGACAAGGTGCGGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTGGAGCCT
CCTGCAGCAGCAGAAGACTGCTGGGAGCAAAATGGACAACTTGTTAAGAGCTACATCAACAACCTTTGGTGGCAGCACGA
GGCGCTGAGCCAGGAGAAGCTGAAGCTGGAGGCAGAGCTTGGCAACATGCAGGGGCTGGGGGAAGACTTCAAGAATAAGT
ACGAGGATGAGATCAACAAGCGAACAGAGATGGAGGGTGAATTTGTCCTCATCAAGAAGGATGTGGATGAAGCTTACATG
AACAAAGTAGAGCTGGAGTCCCGCCTGGAAGGGCTGACTGATGAGATTAACTTCCGCAGGCAGCTATATGAAGTAGAGAT
CCATGAGCTGCAGGCCCAGATCTCAGACATGTCTGTGGTCCTCTCCATGGACAACAGCCGCTCCCTGGACCTGGATGGCA
TCATCGCCGAGGTCAAGGCCCAGTACAAGGAGATCACCAACCGCAGCCGGGCTGAGGCTGAGAGCATATACCAGATCAAG
TACAAGGAGCTGCAAACACTGGCCGGGAAGCGTGGGGATGACCTCCCCACATGCAGACAGATCTCCAAGACGAACCGGAC
CATCAGCCAGCTCTAGGCTGAGATTGAGGGCCTGAAGGGCCAGAGGGCTTCCCTGGAGGCCTCCATTGTGGATGCTGAGC
AGTGTGAGGAGCTGGCTGTTAAGGACGCCAATGCCAAGTTGGCCCAGCTGGAGGCCGCCCTGCACCAGGCCAAGCAGGAC
ACTGCATGGCAGCTGCATGAGTACCAGGAGCTGATGAATGTCAAGCTGGCCCTGGACATCGAGATCGCCACCAACCGCAA
GCTGCTGGAGGGTGAGGAG

Alignment

ORF - retro_chof_2471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.22 %
• Parental protein coverage: 80.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FQSGFGSRASNGFGFGSGVSS---GFGYGGGAGGGFGSTGFPICSSGGIQEVTINQSLLTPLNLQIDPII
          ..SG.G...S..F..GSG.SS.....G.G.G..GG....G....S.GGI..VT.NQSLL.PL.L..DP.I
Retrocopy YTSGSGTCLSSYFRVGSGGSSFQGNLGAGMGLVGGYRGAG----SAGGITTVTLNQSLLSPLKLEVDPNI

Parental  QQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQGSRTVRQNLESLFEA-YLNGLRSQV
          Q.V...E.EQIKTLN.KFASFIDKVRFLE.QNK.LETKW.LLQ.Q...T.......L..A.Y.N.L..Q.
Retrocopy QAVQLQEKEQIKTLNCKFASFIDKVRFLEQQNKMLETKWSLLQQQ--KTAGSKMDNLLRA<YINNLWWQH

Parental  ENTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELVALKKDVDASCMNKVELEAKFNALTEEI
          E.....K.KL..E....Q...ED.K..YEDEIN..T..E.E.V..KKDVD...MNKVELE.....LT.EI
Retrocopy EALSQEKLKLEAELGNMQGLGEDFKNKYEDEINKRTEMEGEFVLIKKDVDEAYMNKVELESRLEGLTDEI

Parental  SFFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAEVKAQYKDIAQRSRAEAESWYQTKYEELQV
          .F...LYE.E....Q.Q.SD.SVVLSMDN.R.LDLD.IIAEVKAQYK.I..RSRAEAES.YQ.KY.ELQ.
Retrocopy NFRRQLYEVEIHELQAQISDMSVVLSMDNSRSLDLDGIIAEVKAQYKEITNRSRAEAESIYQIKYKELQT

Parental  TAGRHSNDLHNTKHEISEMNRTIQTLRAEIGSIKKQCSNLQTAITDAEQCGELALKDARAKLVGLEEALQ
          .AG....DL..T...IS..NRTI..L.AEI...K.Q...L...I.DAEQC.ELA.KDA.AKL..LE.AL.
Retrocopy LAGKRGDDL-PTCRQISKTNRTISQL*AEIEGLKGQRASLEASIVDAEQCEELAVKDANAKLAQLEAALH

Parental  KAKQDMACLLHEYQELMTIKLALEVEIVTH-KLLEGEE
          .AKQD.A..LHEYQELM..KLAL..EI.T..KLLEGEE
Retrocopy QAKQDTAWQLHEYQELMNVKLALDIEIATNRKLLEGEE

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_2471 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,