RetrogeneDB ID: retro_chof_1270

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_24187:6469..7189(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDE1
• Ensembl ID: ENSCHOG00000006004
• Aliases: None
• Description: nudE nuclear distribution E homolog 1 (A. nidulans) [Source:HGNC Symbol;Acc:17619]

Sequence

>retro_chof_1270
GAAAGAAGACTCCGCTCTGAGGAGGAAGAAAGTAACTATTGGGAACTTCTGGCTATGACCTACAAGCCGAGGGCAAGGAA
TACCCAAGAGGAAGTCCGAGGATTCCCAGAGGGAAGTCGAGAATATGGAGCCGAATTGGAGACACAGTTGCAACAAATAG
AAACCGGGGACAGACACCTCATGTCAGAAAATAAACGCCTTCGCATGGAGCTAGAAACTGTCAAGGAGAAGTTTGAAATG
CTGCATTCTGAGGGCTACCGGCAGATCTCAGCCTTAGAGGATGACCTCACACAGACTAAAGCAATTAAAGATCAATTGCA
GAACTATATCTGAGAGTTGGAATAAGCAAATGATGACTTGGAAAGAGTAAAATGGGTCACAGTCATGTCTCTGGAAGACT
TTGAGCAGCTCTGGAATCAAGCCATTGAAAGACATGCCTTCCTGGAGAGAGAACTTGAGAATCTCCGGCAATCTATTAAG
CAACTGAAGGTTAAGGTCAGAGATTTGTGGTCAGAATTGCCCGTGCAGCAGAAGCAGGAGAAACCCAGGACTCCTATGCC
CAGTTCGGTGGAAGCTGAAAGGACGGACATCACTGTCCAGGCTACTGGCTCTCTACCATCTACTCCCATAGGTCACCGAG
GACCCAACTCAAGTTTAAACACATCAGGGACATTGGAGTCCAAACTTGCATCCTCTGGAACTTTGTGTATGATCAGTCCC

Alignment

ORF - retro_chof_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.66 %
• Parental protein coverage: 70.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKTFSSEEEEANYWKDLAMTYKQRAENTQEELREFQEGSREYEAELETQLQQIETRNRDLLSENNRLRME
          .....SEEEE.NYW..LAMTYK.RA.NTQEE.R.F.EGSREY.AELETQLQQIET..R.L.SEN.RLRME
Retrocopy ERRLRSEEEESNYWELLAMTYKPRARNTQEEVRGFPEGSREYGAELETQLQQIETGDRHLMSENKRLRME

Parental  LETIKEKFEMQHSEGYRQISALEDDLTQTKAIKDQLQKYIRELEQANDDLERAKRATIMSLEDFEQRLNQ
          LET.KEKFEM.HSEGYRQISALEDDLTQTKAIKDQLQ.YI.ELE.ANDDLER.K..T.MSLEDFEQ..NQ
Retrocopy LETVKEKFEMLHSEGYRQISALEDDLTQTKAIKDQLQNYI*ELE*ANDDLERVKWVTVMSLEDFEQLWNQ

Parental  AIERNAFLESELDEKENLLESVQRLKDEARDLRQELAVQQKQEKPRTPMPSSVEAERTDTAVQATGSLPS
          AIER.AFLE.EL...ENL..S...LK...RDL..EL.VQQKQEKPRTPMPSSVEAERTD..VQATGSLPS
Retrocopy AIERHAFLEREL---ENLRQSIKQLKVKVRDLWSELPVQQKQEKPRTPMPSSVEAERTDITVQATGSLPS

Parental  TPIAHRGPSSSLNTPGTFRRGLDDSSSGTPLTP
          TPI.HRGP.SSLNT.GT....L..S.......P
Retrocopy TPIGHRGPNSSLNTSGTLESKLASSGTLCMISP

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_1270 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009557	1 retrocopy	retro_amel_104,
Canis familiaris	ENSCAFG00000018722	1 retrocopy	retro_cfam_1579,
Choloepus hoffmanni	ENSCHOG00000006004	1 retrocopy	retro_chof_1270 ,
Cavia porcellus	ENSCPOG00000019614	2 retrocopies	retro_cpor_875, retro_cpor_876,
Ictidomys tridecemlineatus	ENSSTOG00000019896	1 retrocopy	retro_itri_1101,
Tupaia belangeri	ENSTBEG00000005260	1 retrocopy	retro_tbel_1468,