RetrogeneDB ID: retro_chof_2564

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_86533:3064..3630(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006810
• Aliases: None
• Description: None

Sequence

>retro_chof_2564
CATGGCTTGGGCCATGGCTTTGTGAACTATGTGACTGTGGAAGACACAGAAAGAGCAATAAGCATGCTGAATGGCCTGAG
ACTCCAGTTAAAAACCATGAAGGTGTTGTATGCATGCCTGAGCTTAGAGGTCATCAAAGATACCAACTTGTACATCAGTG
GACTTCTGACGACCCAGAAGGACACGGAGGACATGTTCCCTTGGTTTGGATGAATCATCAACTCCTCTGTCCCCATGGAT
CGACCACAGGTTTGTCCAGAGGGGTTGTGTTTATCCAGTTTGACAAATGATCAGAAGCAGAAGAGGCAATTACCAGTTTC
AATGGTCATAATTCCACAGGTTTCTCTGAGCCCATTACAATGAAGTTTGCCGTCAATCCCCACCAGAACAAAAATGTGGC
CTTGTTCTCCCAGTGATACCACTCACCATTTAGACGGTTCTCAGGGCCAGTTCATTACCAGGCACAGAGATTCAGGTTCT
CCCCTACGGGTATTGATCACATGAGTGGGCTTTCTGGTGTAAATGTTCCAGGAAACGCTTCTTCGGGCTGGTGCATCTTC
TTCTGG

Alignment

ORF - retro_chof_2564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.04 %
• Parental protein coverage: 71.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSR
          H.LG.GFVNYVT..D.ERAI..LNGLRLQ.KT.KV.YA..S.EVIKD.NLYISGL....TQKD.EDMF..
Retrocopy HGLGHGFVNYVTVEDTERAISMLNGLRLQLKTMKVLYACLSLEVIKDTNLYISGL--LTTQKDTEDMFPW

Parental  FGRIINSRVLVDQ-TTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFAANPNQNKNVALLS
          FG.IINS.V..D..TTGLSRGV.FI.FDK.SEAEEAITSFNGH...G.SEPIT.KFA.NP.QNKNVAL.S
Retrocopy FG*IINSSVPMDR<TTGLSRGVVFIQFDK*SEAEEAITSFNGHNSTGFSEPITMKFAVNPHQNKNVALFS

Parental  QLYHSPARRFGGPVHHQAQRFRFSPMGVDHMSGLSGVNVPGNASSGWCIFIY
          Q.YHSP.RRF.GPVH.QAQRFRFSP.G.DHMSGLSGVNVPGNASSGWCIF..
Retrocopy Q*YHSPFRRFSGPVHYQAQRFRFSPTGIDHMSGLSGVNVPGNASSGWCIFFW

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_2564 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018353	1 retrocopy	retro_cfam_1972,
Choloepus hoffmanni	ENSCHOG00000002464	1 retrocopy	retro_chof_1943,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Choloepus hoffmanni	ENSCHOG00000006810	2 retrocopies	retro_chof_2564 , retro_chof_44,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Tupaia belangeri	ENSTBEG00000015038	1 retrocopy	retro_tbel_3670,