RetrogeneDB ID: retro_chof_1685

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_35874:9350..9921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSCHOG00000007254
• Aliases: None
• Description: chloride channel, nucleotide-sensitive, 1A [Source:HGNC Symbol;Acc:2080]

Sequence

>retro_chof_1685
CTGGCTTGGTTAGATGACCCTGGGTTAGAGATCTCTGGAATAGCCACCGTTAGCTGACACAGTGTGTCCAGGGACCTAAG
TGCCTATCCACGAGAGCATCTGCATGTTATGGTGAATACCAGATTTGGAGAAGAATCAAAAGGATCTGTTGATGATGAAG
AAGAGGAAGACAGTGATGTGATGATGAACCTATTGCTGAGTTCAGTTTTGTGCCTACTGATAAATCAGCATTGGAAGCAC
AGTTCATGCAATGTGTGCGTGCCAAGCTTTGCATCCAGATCCTGAGGATGAAGACTCAGATGATTATGTTGGAGAAGAGT
ATGATGTGGAGCACATGAACAAGGGCAGGGGGACATCCCTACATTTTACACCAGTGAAGGACTTATCCGATTTGACAGCA
GAGGGCCACGCCACATTAGAGAGATTGGTAGGAATGCTTTCTCGGTGTGTGAGCAACCAGTATAACGTGGCTGGGGTCCG
GACCGAAGACCTGAAAAGAGATTATGAAGATGGGATGGAGGTAGATAGCACAACCGTTGTTGGACAGTTTGAGGATGCAG
ATGTTGATCAC

Alignment

ORF - retro_chof_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.88 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSWLDGSGLGFSLEYPTISLHAVSRDLSAYPREHLYVMVNAKFGEESKESVADEEEEDSDDD-DDEPIAE
          L.WLD..GL..S....T.S.H.VSRDLSAYPREHL.VMVN..FGEESK.SV.D.EEE...D..DDEPIAE
Retrocopy LAWLDDPGLEIS-GIATVS*HSVSRDLSAYPREHLHVMVNTRFGEESKGSV-DDEEEEDSDV<DDEPIAE

Parental  FRFVPSDKSALEAMFT-AMCECQALHPDPEDEDSDDYDGEEYDVE-AHEQGQGDIPTFYTYEEGL-SHLT
          F.FVP.DKSALEA.F..AMC.CQALHPDPEDEDSDDY.GEEYDVE.AHEQGQGDIPTFYT..EGL.S.LT
Retrocopy FSFVPTDKSALEAQFM<AMCACQALHPDPEDEDSDDYVGEEYDVE<AHEQGQGDIPTFYT-SEGL>SDLT

Parental  AEGQATLERLEGMLSQSVSSQYNMAGVRTEDSIRDYEDGMEVDTTPTVAGQFEDADVDH
          AEG.ATLERL.GMLS..VS.QYN.AGVRTED..RDYEDGMEVD.T.TV.GQFEDADVDH
Retrocopy AEGHATLERLVGMLSRCVSNQYNVAGVRTEDLKRDYEDGMEVDST-TVVGQFEDADVDH

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_1685 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Choloepus hoffmanni	ENSCHOG00000007254	1 retrocopy	retro_chof_1685 ,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Dasypus novemcinctus	ENSDNOG00000008188	1 retrocopy	retro_dnov_477,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Myotis lucifugus	ENSMLUG00000024623	2 retrocopies	retro_mluc_1501, retro_mluc_1507,
Mustela putorius furo	ENSMPUG00000015944	1 retrocopy	retro_mputfur_435,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Tupaia belangeri	ENSTBEG00000001316	1 retrocopy	retro_tbel_2975,