RetrogeneDB ID: retro_chof_322

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_732:99452..100604(+)
• 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_322
TACACGAGCGGGTCCGGCACCTGCCTCAGCTCCTACTTTAGGGTGGGCAGCGGCGGCAGCAGCTTCCAGGGCAACCTGGG
TGCTGGCATGGGTCTGGTGGGGGGCTACAGAGGGGCAGGGAGTGCAGGGGGCATCACAACTGTCACGTTGAACCAGAGCC
TGCTGAGCCCCCTTAAGCTGGAGGTGGACCCCAACATCCAGGCTGTTCAGTTGCAAGAGAAGGAGCAGATCAAGACCCTC
AACTGCAAGTTTGCTTCCTTCATTGACAAGGTGCAGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTGGAGCCT
CTTGGAGCAGCAGAAGATGGCTGGGAACAAAATGGACAACTTGTTCGAGAGCTACATCAACAACCTTTGGCGGCAGCACA
AGGTGCTGAGCCAGGAGAAGCTGAAGCTGGAGGCAGAGCTTGGCAACATGCAGGGGCTGGTGGAAGACTTCAAGAATAAG
TAAGAGGATGAGATCAACAAGCGAACAGAGATGGAGGGTGAATTTGTCCTCATCAAGAAGGATGTGGATGAAGCTTACAT
GAACAAAGTAGAGCTGGAGTCCCGCCTGGAAGGGCTGACCGATGAAATTAACTTCCTCAGGCAGCTGTGTGAAGAGGAGA
TCTGTGAGCTGCAGGCCCAGATCTTGGACATGTCTGTGGTCCTCTCCATGGACAACAGCCGCTCCCTGGACCTGGATGGC
ATCATCGCCGAGGTCAAGGCCCAGTACAAGGAGATCACCAACCGCAGCCGGGCTGAGGCTGAGAGCACGTACCAGATCAA
GTACCAGGAGCTGCAGACGCTGGCTGGGAAACATGGGGATGACCTCCACCGCACGAAGATGGAGATCTCCGAGATAAACT
GGACCATCAGCGGTCTCCAGGCTGAGATTGAGGGCCTGAAGGGCCAGAGGGCTTCCCTGGAGGCCGCCATTGTGGATGCT
GAGCAGTGTGAGGAGCTGGCTGTTAAGGACGCCAATGCCAAGTTGGCCCAGCTGGAGGCCGCCCTGCACCAGGCCAAGCA
GGACACTGCATGGCAGCTGCACGAGTACCAGGAGCTGATGAACGTCAAGCTGGCCCTGGACATCGAGATCGCCACCAACC
GCAAGCTGCTGGAGGGCGAGGAGAGCCGGCTG

Alignment

ORF - retro_chof_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.18 %
• Parental protein coverage: 80.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

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  QQVRKEEWEQIKTLNNKFASFIDKVRFLEEQNKVLETKWNLLQEQGSRTVRQNLESLFEAYLNGLRSQVE
          Q.V...E.EQIKTLN.KFASFIDKV.FLE.QNK.LETKW.LL..Q...........LFE.Y.N.L..Q..
Retrocopy QAVQLQEKEQIKTLNCKFASFIDKVQFLEQQNKMLETKWSLLEQQ--KMAGNKMDNLFESYINNLWRQHK

Parental  NTTIKKDKLDTEMRKVQDIMEDVKVRYEDEINRHTAAENELVALKKDVDASCMNKVELEAKFNALTEEIS
          .....K.KL..E....Q...ED.K...EDEIN..T..E.E.V..KKDVD...MNKVELE.....LT.EI.
Retrocopy VLSQEKLKLEAELGNMQGLVEDFKNK*EDEINKRTEMEGEFVLIKKDVDEAYMNKVELESRLEGLTDEIN

Parental  FFHMLYETELSHMQTQVSDTSVVLSMDNNRCLDLDSIIAEVKAQYKDIAQRSRAEAESWYQTKYEELQVT
          F...L.E.E....Q.Q..D.SVVLSMDN.R.LDLD.IIAEVKAQYK.I..RSRAEAES.YQ.KY.ELQ..
Retrocopy FLRQLCEEEICELQAQILDMSVVLSMDNSRSLDLDGIIAEVKAQYKEITNRSRAEAESTYQIKYQELQTL

Parental  AGRHSNDLHNTKHEISEMNRTIQTLRAEIGSIKKQCSNLQTAITDAEQCGELALKDARAKLVGLEEALQK
          AG.H..DLH.TK.EISE.N.TI..L.AEI...K.Q...L..AI.DAEQC.ELA.KDA.AKL..LE.AL..
Retrocopy AGKHGDDLHRTKMEISEINWTISGLQAEIEGLKGQRASLEAAIVDAEQCEELAVKDANAKLAQLEAALHQ

Parental  AKQDMACLLHEYQELMTIKLALEVEIVTH-KLLEGEECRL
          AKQD.A..LHEYQELM..KLAL..EI.T..KLLEGEE.RL
Retrocopy AKQDTAWQLHEYQELMNVKLALDIEIATNRKLLEGEESRL

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_322 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,