RetrogeneDB ID: retro_chof_1485

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_305043:414..736(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL1
• Ensembl ID: ENSCHOG00000008609
• Aliases: None
• Description: myosin, light chain 1, alkali; skeletal, fast [Source:HGNC Symbol;Acc:7582]

Sequence

>retro_chof_1485
GGGGACATGATGAAGGCCTGGGCCAGGAGCTCCCCAGTGCCGAGGTGCTCAAGGTCCTGGGGACCCCCAGGAGTGATGAG
ATGAATGTGAAGGTACCGGACTTTGAGCACTTCTCGTCCTGCTAAGGACCATGGCTAAGAACAAGGACCAGGGCACCCAT
GAGGATTATGTGGAAGGTCTTTGAGTCATCGTTGTCTTTGACAAGGATGGGAATGGCACCATCATGGGCACTGAAATCCA
ACATGTCACCCTGGGTGAGGTGACAGAGGAAAAAGTAGAGATGCTGGTGGCAGGACACAAGGAAGGCAATGTTTGTATCA
AC

Alignment

ORF - retro_chof_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.1 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GDVLRA-LGTNPTNAEVKKVLGNPSNEELKAKKIEFEQF-LPMLQAISNNKDQGTYEDFVEGL---RVFD
          GD...A.LG.....AEV.KVLG.P...E...K...FE.F.L..L.....NKDQGT.ED.VEGL....VFD
Retrocopy GDMMKA<LGQELPSAEVLKVLGTPRSDEMNVKVPDFEHF<LVLLRTMAKNKDQGTHEDYVEGL*VIVVFD

Parental  KEGNGTVMGAELRHVLATLGEKMKEEEVEALMAGQEDSNGCIN
          K.GNGT.MG.E..HV..TLGE...EE.VE.L.AG....N.CIN
Retrocopy KDGNGTIMGTEIQHV--TLGE-VTEEKVEMLVAGHKEGNVCIN

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_1485 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008609	2 retrocopies	retro_chof_1485 , retro_chof_2467,
Choloepus hoffmanni	ENSCHOG00000013199	1 retrocopy	retro_chof_2215,
Macropus eugenii	ENSMEUG00000006905	5 retrocopies	retro_meug_1796, retro_meug_21, retro_meug_537, retro_meug_87, retro_meug_914,
Mus musculus	ENSMUSG00000061816	1 retrocopy	retro_mmus_973,
Sorex araneus	ENSSARG00000002568	1 retrocopy	retro_sara_196,
Tarsius syrichta	ENSTSYG00000007599	3 retrocopies	retro_tsyr_1284, retro_tsyr_1539, retro_tsyr_2003,