RetrogeneDB ID: retro_chof_1810

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_39118:6557..7356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNB4
• Ensembl ID: ENSCHOG00000001961
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), beta polypeptide 4 [Source:HGNC Symbol;Acc:20731]

Sequence

>retro_chof_1810
CTACTAGTCAGTGCTTCCCAAGATGGAAAATTAATTATTTTGGATAGTTCTACAACAAATAAGATGCATGCTATTCCTTT
GAGATCCTCCTGTGCTTATGCCCCCTCTGGTAATTATGTTGTTTGTGGGGGACTGGACAATATCTGTTCTATTTACAACT
TAAAAACCAGGGAGGGAAATGTGAGAGTTAGCCAAGAGTTACCAGGTCACACAGGCTACTTGTCCTGCTGTCATTTTTTA
GATGACAGCCAAATTGTTACAAGTTCAGTAGAAACAACTTGTTCTTTATGGGATGTGGGAACTGCCCAGTAGACCACACC
CACTGGGCATTCTGGGGATGTGATGAGTCTTTCTCTAAGTCCTGACATGAGGACTTTCATTCCTGGTGCTTGCGATGCCT
CTTCCAAACTATGGGATATTCGAGATGGAATGTGTAAACAGTCTTTCACTGGACACGTGTTGGATATTAATGCTGTCAGT
TTTTTCCCAAATGGATATGCCTTTACCATTGGCTCTGATGATGCCACTTGACAGCTCTTTGACCTTCACACAGACCAAGA
GTTCTTACTGTACTCTCATGACAATATCATCTGTGGAATCACTTCTGTAGCCTTCTCAAATAGTGGGTGCCTCCTGTTAG
CTGGTTGTGATGACTTTAATTGTAATGTGGGGAACAAGCTACAAGGAGATTGTGCAGGGTCCTTGCTGGTCATGACAACC
ATGTGGCTGTGTAGGTGTAACTGATGATGGCTTGACTGTGGCAACAGGCTCTTGGGATAGTTTTTTTAGAATCTGAAAT

Alignment

ORF - retro_chof_1810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 80.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLVSASQDGKLIIWDSYTTNKMHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRE
          LLVSASQDGKLII.DS.TTNKMHAIPLRSS....CAYAPSGNYV.CGGLDNICSIYNLKTREGNVRVS.E
Retrocopy LLVSASQDGKLIILDSSTTNKMHAIPLRSS----CAYAPSGNYVVCGGLDNICSIYNLKTREGNVRVSQE

Parental  LPGHTGYLSCCRFLDDSQIVTSSGDTTCALWDIETAQQTTTFTGHSGDVMSLSLSPDMRTFVSGACDASS
          LPGHTGYLSCC.FLDDSQIVTSS..TTC.LWD..TAQ.TT..TGHSGDVMSLSLSPDMRTF..GACDASS
Retrocopy LPGHTGYLSCCHFLDDSQIVTSSVETTCSLWDVGTAQ*TTP-TGHSGDVMSLSLSPDMRTFIPGACDASS

Parental  KLWDIRDGMCKQSFTGHVSDINAVSFFPNGYAFATGSDDATCRLFDLRADQELLLYSHDNIICGITSVAF
          KLWDIRDGMCKQSFTGHV.DINAVSFFPNGYAF..GSDDAT..LFDL..DQE.LLYSHDNIICGITSVAF
Retrocopy KLWDIRDGMCKQSFTGHVLDINAVSFFPNGYAFTIGSDDAT*QLFDLHTDQEFLLYSHDNIICGITSVAF

Parental  SKSGRLLLAGYDDFNCNVWDTLKGDRAG-VLAGHDNRVS-CLGVTDDGMAVATGSWDSFLRIWN
          S.SG.LLLAG.DDFNCNV...L.GD.AG.VLAGHDN.V..C.GVTDDG..VATGSWDSF.RI.N
Retrocopy SNSGCLLLAGCDDFNCNVGNKLQGDCAG<VLAGHDNHVA<CVGVTDDGLTVATGSWDSFFRI*N

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_1810 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001961	1 retrocopy	retro_chof_1810 ,
Myotis lucifugus	ENSMLUG00000007640	1 retrocopy	retro_mluc_2178,