RetrogeneDB ID: retro_chof_9

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_28389:6859..7939(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000002558
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000005553
• Aliases: None
• Description: None

Sequence

>retro_chof_9
ATGATCCAGGGGCGTGGAAAATATGATTTTTATATTGGTCTGGGATTGGCTATGAGCTCCAGCATTTTCATTGGAGGGAG
TTTCATTTTGAAAAAGAAAGGTCTCCTGCGACTTGCCAGAAAAGGCTCCATGAGAGCAGGTCAAGGCGGCCATGCGTATC
TTAAAGAATGGTTGTGGTGGGCTGGACTGCTATCAATGGGAGCTGGTGAGGTGGCCAACTTCGCTGCGTATGCGTTTGCT
CCGGCCACGTTGGTGACTCCGCTGGGAGCGCTCAGTGTCCTAGTGAGTGCCATTCTTTCTTCATACTTTCTAAATGAAAG
ACTTAATCTTCACGGGAAAATTGGGTGTCTGTTAAGTATTCTAGGGTCTACAGTTATGGTCATTCATGCTCCAAAGGAAG
AGGAGATAGAGACCTTAAATGAGATGTCTCACAAGCTGGGTGATCCAGGTTTTGTGGTCTTTGCCACCCTTGTGGTCATT
GTGTCCTTGATATTAATCTTCATAGTGGGACCCGGCCATGGACAGACCAACGTTCTCGTGTATATAACAATCTGCTCTGT
GATCGGAGCATTTTCGGTGTCCTGTGTCAAAGGCCTGGGCATCGCTATTAAAGAACTGCTTGCTGGAAAGCCCGTGCTGC
AGCACCCGCTGGCCTGGGCCCTGCTGCTGAGCCTGGTGGTGTGTGTGAGCACACAGATCAATTACCTAAACAGGGCCCTG
GACATATTCAACACCTCCATTGTGACGCCCATTTATTACGTGTTCTTCACAACATCGGTTTTAACTTGTTCAGCTATTCT
TTTTAAGGAGTGGCAGAATATGCCTGTTGACGATGTCATTGGTACTTTGAGCGGCTTCCTTACCATCATTGTGGGCATAT
TTTTATTGCATGCCTTTAAAGATCTCAGTTTTAGTCTAGCAAGTCTGCCATTGTCTTTTCGAAAAGATGAGAAAGTAATG
AATGGCAATCCCTCCAATATGTATGAAATTCTTAATAATAACGAAGAAAGCTTAACCTGTGGAGTTGAACGCACTAGTGA
AAGTATCTCCCGAAGAAATGGAAACCTGGCAGCTTTTTAA

Alignment

ORF - retro_chof_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIQGRGKYDFYIGLGLAMSSSIFIGGSFILKKKGLLRLARKGSMRAGQGDRAYLKEWLWWAGLLSMGAGE
          MIQGRGKYDFYIGLGLAMSSSIFIGGSFILKKKGLLRLARKGSMRAGQG..AYLKEWLWWAGLLSMGAGE
Retrocopy MIQGRGKYDFYIGLGLAMSSSIFIGGSFILKKKGLLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGAGE

Parental  VANFAAYAFAPATLVTPLGALSVLVSAILSSYFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEEIETLN
          VANFAAYAFAPATLVTPLGALSVLVSAILSSYFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEEIETLN
Retrocopy VANFAAYAFAPATLVTPLGALSVLVSAILSSYFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEEIETLN

Parental  EMSH-LGDPGFVVFATLVVIVSLILIFIVGPRHGQTNVLVYITICSVIGAFSVSCVKGLGIAIKELLAGK
          EMSH.LGDPGFVVFATLVVIVSLILIFIVGP.HGQTNVLVYITICSVIGAFSVSCVKGLGIAIKELLAGK
Retrocopy EMSHKLGDPGFVVFATLVVIVSLILIFIVGPGHGQTNVLVYITICSVIGAFSVSCVKGLGIAIKELLAGK

Parental  PVLQHPLAWALLLSLVVCVSTQINYLNRALDIFNTSIVTPIYYVFFTTSVLTCSAILFKEWQNMPVDDVI
          PVLQHPLAWALLLSLVVCVSTQINYLNRALDIFNTSIVTPIYYVFFTTSVLTCSAILFKEWQNMPVDDVI
Retrocopy PVLQHPLAWALLLSLVVCVSTQINYLNRALDIFNTSIVTPIYYVFFTTSVLTCSAILFKEWQNMPVDDVI

Parental  GTLSGFLTIIVGIFLLHAFKDLSFSLASLPLSFRKDEKVMNGNPSNMYEILNNNEESLTCGVERTSESIS
          GTLSGFLTIIVGIFLLHAFKDLSFSLASLPLSFRKDEKVMNGNPSNMYEILNNNEESLTCGVERTSESIS
Retrocopy GTLSGFLTIIVGIFLLHAFKDLSFSLASLPLSFRKDEKVMNGNPSNMYEILNNNEESLTCGVERTSESIS

Parental  RRNGNLAAF
          RRNGNLAAF
Retrocopy RRNGNLAAF

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_9 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9 ,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,