RetrogeneDB ID: retro_chof_1282

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_248268:264..1176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCMF1
• Ensembl ID: ENSCHOG00000005786
• Aliases: None
• Description: potassium channel modulatory factor 1 [Source:HGNC Symbol;Acc:20589]

Sequence

>retro_chof_1282
TCTGTAGCTTGCCACTATTGTGGAAAAATGGGCTATACGGAGACATCTCTTCAAGAACATATTACTTCTGAACACACAGA
AACATCAACAGAAGTGATCTGTTCGACCTGTGTAGCATTACCTGGAGGCGATCCTAACCATGTCACGGACGACTTTGCAG
GTCACCTTACACTTGAACACAGAGCCCACAGAGATTTAGATGAATCCAGTGGTGTTCAACACGTACACAGAATATTTCAT
CCTGGCTGGGGCTTAGGAGGTCCTCAAGCTCAGATATCAAAGATGCACCTTACTAGCAGCTCTACTGGTGGACTTTCTTC
ACAGGGTTCATATTCCCCAAGCAGTAGGAAAGCCATGGATCCTATAGCTGAGCTCTTATCTCAGTTATCAGGAGTGAGAT
GTTCTGCAGGAGGACAGCTTAACTCCTCAGGTCCTTCCGCCTCTCAGTTATAGCAACTGCAGATGCAGCTGCAACTAGAG
AGGCAGCACGCCCAGGCAGCACGGCAAAAACTGGAGACAGCTCACGACACAACACGGCACACTAACACAAGCAGCATCAC
CACTACAATCACACAATCCACAGCAACAATCAACACATCTAACAAAGAGAGAAGTCAGCAAATGCTCCAGAATTCACAAT
TTCTTTTAACGAGGTTGAATGACCCTAAACTGTCTGAAACAGAGTGCCAGTCCACGGAAAGCAAGTGTGCAGAACACAGC
CTGTTTGTTCAAGAGATCCTTCAGTCCACTTTAGTGCACGAAGAGAGCTAGTCCTCAGACGAGGATGAACGGAGGCAGAT
GGCAGATCTCGATGCTATGGGTTGTGTAGATATTATGCCTTTAGATATTGCTTTAGAAAACCTAAATTTAAAAGAGAGTA
ATAAAGGAAATGAGCCTCCACCACCTCTTCTT

Alignment

ORF - retro_chof_1282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.03 %
• Parental protein coverage: 80.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFTCPYCGKMGYTETSLQEHVTSEHAETSTEVICPICAALPGGDPNHVTDDFAAHLTLEHRAPRDLDESS
          S..C.YCGKMGYTETSLQEH.TSEH.ETSTEVIC..C.ALPGGDPNHVTDDFA.HLTLEHRA.RDLDESS
Retrocopy SVACHYCGKMGYTETSLQEHITSEHTETSTEVICSTCVALPGGDPNHVTDDFAGHLTLEHRAHRDLDESS

Parental  GVRHVRRMFHPGRGLGGPRARRSNMHFTSSSTGGLSSSQSSYSPSSREAMDPIAAELLSQLSGVRRSAGG
          GV.HV.R.FHPG.GLGGP.A..S.MH.TSSSTGGLSS.Q.SYSPSSR.AMDPIA.ELLSQLSGVR.SAGG
Retrocopy GVQHVHRIFHPGWGLGGPQAQISKMHLTSSSTGGLSS-QGSYSPSSRKAMDPIA-ELLSQLSGVRCSAGG

Parental  QLNSSGPSASQLQQLQMQLQLERQHAQAARQQLETARNATRRTNTGSVTTTITQSTAATNTANTESSQQT
          QLNSSGPSASQL.QLQMQLQLERQHAQAARQ.LETA...TR.TNT.S.TTTITQSTA..NT.N.E.SQQ.
Retrocopy QLNSSGPSASQL*QLQMQLQLERQHAQAARQKLETAHDTTRHTNTSSITTTITQSTATINTSNKERSQQM

Parental  LQNSQFLLTRLNDPKMSETERQSVESERADRSLFVQELLLSTLVREESSSSDEDERGEMADFGAMGCVDI
          LQNSQFLLTRLNDPK.SETE.QS.ES..A..SLFVQE.L.STLV.EES.SSDEDER..MAD..AMGCVDI
Retrocopy LQNSQFLLTRLNDPKLSETECQSTESKCAEHSLFVQEILQSTLVHEES*SSDEDERRQMADLDAMGCVDI

Parental  MPLDVALENLNLKESNKGNEPPPPPL
          MPLD.ALENLNLKESNKGNEPPPP.L
Retrocopy MPLDIALENLNLKESNKGNEPPPPLL

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_1282 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005786	1 retrocopy	retro_chof_1282 ,
Dasypus novemcinctus	ENSDNOG00000006752	2 retrocopies	retro_dnov_1000, retro_dnov_2063,
Echinops telfairi	ENSETEG00000001809	1 retrocopy	retro_etel_1685,
Myotis lucifugus	ENSMLUG00000000979	1 retrocopy	retro_mluc_1781,
Monodelphis domestica	ENSMODG00000015567	1 retrocopy	retro_mdom_1682,
Otolemur garnettii	ENSOGAG00000034863	2 retrocopies	retro_ogar_3140, retro_ogar_397,
Vicugna pacos	ENSVPAG00000010386	1 retrocopy	retro_vpac_650,