RetrogeneDB ID: retro_chof_407

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_104696:3060..3743(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YAP1
• Ensembl ID: ENSCHOG00000001095
• Aliases: None
• Description: Yes-associated protein 1 [Source:HGNC Symbol;Acc:16262]

Sequence

>retro_chof_407
CACATTGATCAGACAAGACATGGAAGGACCCCAGGAAGGCCATGCTCTTTCAGGTGAAGGTGACTGCCCCCACCAGTCCT
CCAGGGCAGCAGAATTTGATGAACACCGCCTCCCGTCCTCTTCCTGATGGATGGGAGCAAGCCATGATTCAGGATGGAGA
AATTTACTATATAAACCATAAAAACAAGACCATCTCTTGGCTAGACCCAAAGCTTGACCCTTATTTGGTCATGAACCAGA
CAGTCAGGGTGCTCCGGTGAAACAGCCAGCACCCCTGGTTCCCCGGAGCCCCAGGGAGGAGTTATGGGTGCAGAAACTCC
AATCAGCAGCAGCAGATGAGGCTTCAGCAACTGCAGATGGAGAAAGAGAGACTGTGACAGAAGCAGGAAGATCTGCTTCA
GCAGGCAATAAGGAATATCAATCCCAGCAGAGCAAATTCTCCAAAATGTCAGGAATTAGCTCATGATAGCCAGTTACTGA
CACTGGAGCAGGATGAAGGGACTCAAAACCCAGTATCTTCTCTGGAGGTGTCTCAGATACTGAGAGCAATGACAACTAAT
AGCTCAGACCTCTTTCTTAACAGTGGCACCTAGAACCCTTGAGATGAGAATACAGACAGTGGATGAAGCCTGAGCAGCTA
CAGTGTCTCTCAAAGTTCAGATGTCTTCCTGAATGGTGTTGAT

Alignment

ORF - retro_chof_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 73.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HIDQTT-TWQDPRKAMLSQLNVTAPTSPPVQQNMMNAASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLD
          HIDQT..TW.DPRKAML.Q..VTAPTSPP.QQN.MN.AS.PLPDGWEQAM.QDGEIYYINHKNKT.SWLD
Retrocopy HIDQTR<TWKDPRKAMLFQVKVTAPTSPPGQQNLMNTASRPLPDGWEQAMIQDGEIYYINHKNKTISWLD

Parental  PRLD-PRFAINQRISQSAPVKQPPPLAPQSP-QGTVMGGG-NSNQQQQMRLQQLQMEKERLRLKQQELLR
          P.LD.P.F......SQ.APVKQP.PL.P.SP.QG.VMG...NSNQQQQMRLQQLQMEKERL..KQ..LL.
Retrocopy PKLD<PLFG-HEPDSQGAPVKQPAPLVPRSP<QGGVMGAE<NSNQQQQMRLQQLQMEKERL*QKQEDLLQ

Parental  QAMRNINPSTANSPKCQELALRSQLPTLEQDGGTQNPVSSPGMSQELRTMTTNSSDPFLNSGTYHSRDES
          QA.RNINPS.ANSPKCQELA..SQL.TLEQD.GTQNPVSS...SQ.LR.MTTNSSD.FLNSGT....DE.
Retrocopy QAIRNINPSRANSPKCQELAHDSQLLTLEQDEGTQNPVSSLEVSQILRAMTTNSSDLFLNSGT*NP*DEN

Parental  TDSGLSMSSYSVPRTPDDFLNSVD
          TDSG.S.SSYSV....D.FLN.VD
Retrocopy TDSG*SLSSYSVSQSSDVFLNGVD

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_407 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001095	2 retrocopies	retro_chof_1687, retro_chof_407 ,
Callithrix jacchus	ENSCJAG00000000627	1 retrocopy	retro_cjac_4112,