RetrogeneDB ID: retro_chof_44

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_14754:8565..9270(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000002832
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_chof_44
GTGTCATACGCACGCCCGAGCTCAGAGGTCATCAAAGATGCCAACTTATACATCAGTGGACTCCCGAGGACCATGACCCA
GAAAGACGTGGAGGACATGTTCTCTCGGTTTGGACGAATCATCAACTCCCGTGTCCTCGTGGATCAGACCACAGGTTTGT
CCAGAGGGGTTGCGTTTATCCGGTTTGACAAACGATTGGAAGCAGAAGAGGCAATTACCAGTTTCAGTGGTCATAAACCC
TCAGGTTCCTCCGAGCCCATTACAGTGAAGTTTGCGGCCAATCCCAACCAGAACAAAAATGTGGCGTTGCTCTCCCAGCT
GCACCACTCGCCAGCTAGACGGTTCGGAGGGCCAGTTCATCACCAGGCACAGAGATTCAGGTTCTCCCCTATGGGTGTAG
ATCACATGAGTGGGCTTTCTGGTGTAAATGTCCCAGGAAACGCTTCTTCAGGCTGGTGCATCTTCATCTACAACCTTGGT
CAGGATGCTGATGAGGGAATCCTCTGGCAGATGTTTGGCCCCTTTGGCACAGTGACCAATGTGAAAGTGATTCGTGATTT
CAACACCAACAAGTGCAAAGGGTTTGGTTTTGTGATGATGACAAACTATGAAGAAGCTGCGATGGCCATAGCAAGTCTGA
ACGGCTACCGCCTGGGGGACAAAATCTTACAGGTTTCCTTCAAGACCAACAAGTCCCACAAATAA

Alignment

ORF - retro_chof_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.44 %
• Parental protein coverage: 87.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE
          VSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKR.EAEE
Retrocopy VSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRLEAEE

Parental  AITSFNGHKPPGSSEPITVKFAANPNQNKNVALLSQLYHSPARRFGGPVHHQAQRFRFSPMGVDHMSGLS
          AITSF.GHKP.GSSEPITVKFAANPNQNKNVALLSQL.HSPARRFGGPVHHQAQRFRFSPMGVDHMSGLS
Retrocopy AITSFSGHKPSGSSEPITVKFAANPNQNKNVALLSQLHHSPARRFGGPVHHQAQRFRFSPMGVDHMSGLS

Parental  GVNVPGNASSGWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI
          GVNVPGNASSGWCIFIYNLGQDADEGILWQMFGPFG.VTNVKVIRDFNTNKCKGFGFV.MTNYEEAAMAI
Retrocopy GVNVPGNASSGWCIFIYNLGQDADEGILWQMFGPFGTVTNVKVIRDFNTNKCKGFGFVMMTNYEEAAMAI

Parental  ASLNGYRLGDKILQVSFKTNKSHK
          ASLNGYRLGDKILQVSFKTNKSHK
Retrocopy ASLNGYRLGDKILQVSFKTNKSHK

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_44 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,