RetrogeneDB ID: retro_chof_2310

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_65173:4954..6392(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2B1
• Ensembl ID: ENSCHOG00000010864
• Aliases: None
• Description: adaptor-related protein complex 2, beta 1 subunit [Source:HGNC Symbol;Acc:563]

Sequence

>retro_chof_2310
ATGACTGACTCCAAGTACTTTACAACCAATAAAAAAGGAGAAATCTTTGAATTAAAGGCTGAACTTAACAATGAAAAGAA
AGAAAAGAGGAAGGAGGCTGTGAAGAAAGTGATTGCTGCTATGACCGTGGGGAAAGATGTTAGCTCTCTCTTTCCAGATG
TAGTGAACTGTATGCAGACTGACAACCTGGAACTCAAGAAGCTTGTGTATCTCTATTTGATGAATTATGCCAAGAGCCAG
CCAGACATGGCCATCATGGCTGTCAGTAGCTTTGTGAAGGACTGTGAAGATCCCAATCCTTTGATTTGGGCCTTGGCCAT
CAGAACCATGGGGTGCATCCCAGTCGACAAGATTACTGAATATCTTTGTGAGCCCCTCCGCAAATGCTTGAAGGATGAAG
ATCCCTATGTTCGGAAAACAGCAGCAGTCTGCGTGGCAAAGCTCCATGATATCAATGCCCAAATGGTGGAAGATCAGGGA
TTTCTGGATTCTCTGCGAAATCTCATAGCAGATTCAAATCCAATGGTGGTGGCTAATGCTGTAGCAGCATTATCTGAAAT
CAGTGAGTCTCACCCAAATAGCAACTTACTGGATCTACACCCACAGAACATTAATAAGCTGCTGACAGCCCTGAATGAGT
GCACTGAGTGGGGCCAGATTTTCTTCCTAGACTGCCTGTCTAATTACAACCCTAAAGATGACCGGGAGGCTCAGAGCATC
TGTGAGCGGGTAACTCCCTGGCTATCCCATGCCAACTCAGCAGTGGTGCTCTCAGCAGTAAAAGTCATAATGAAATTTCT
AGAATTGTTACCCAAGGACTCTGACTACTACAATATGCTGCCGAAGAAGTTAGCCCCTCCTCTTGTCACTTTGCTGTCTG
GGGAGCCAGAGGTGCAATATGTCGCCCTGAGGAACTTCAACCTCATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAG
AATCAAAGTCTTCTTTGTGAAGTACAATGATCCCATCTATGTTAAACTAGAGAAGTTGGACATCATGATTCGCTTGGCAT
CCCAAGCCAACATTGCTCAGGTTCTGGCAGAACTGAAAGAATATGCCACAGAGGTGGATGTTGACTTTGTTCGCAAAGCT
GTGCAAGCCATTGGACGGTGTGCCATCAAGGTGGAGCAATCTGCAGAACGCTGTGTGAGCACATTGCTTGATCTCATCCA
GACGAAAGTAAATTATGTGGTCCAAGAGGCAATTGTTGTCATCAGAGACATCTTCCGCAAATATCCCAACAAATATGAAA
GTATCATTGCCACTCTTTGTGAGAACCTAGACTCACTGGATGAGCCAGATGCTCGAGCAGCTATGATTTGGATTGTGGGA
GAATTTGCTGAAAGGATTGACAATGCAGATGAGTTACTAGAGAGCTTCTTGGAAGGCTTTCATGATGAAAGCACCCAG

Alignment

ORF - retro_chof_2310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 50.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
Retrocopy MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQPDMAIMAV.SFVKDCEDPNPLI.ALA.RTMGCI.VDKITEYLCEPLRKCLKDEDPYVRKT
Retrocopy LYLMNYAKSQPDMAIMAVSSFVKDCEDPNPLIWALAIRTMGCIPVDKITEYLCEPLRKCLKDEDPYVRKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLHDINAQMVEDQGFLDSLR.LIADSNPMVVANAVAALSEISESHPNSNLLDL.PQNINKLLTA
Retrocopy AAVCVAKLHDINAQMVEDQGFLDSLRNLIADSNPMVVANAVAALSEISESHPNSNLLDLHPQNINKLLTA

Parental  LNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNML
          LNECTEWGQIF.LDCLSNYNPKDDREAQSICERVTP.LSHANSAVVLSAVKV.MKFLELLPKDSDYYNML
Retrocopy LNECTEWGQIFFLDCLSNYNPKDDREAQSICERVTPWLSHANSAVVLSAVKVIMKFLELLPKDSDYYNML

Parental  LKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQE-IKVFFVKYNDPIYVKLEKLDIMIRLASQA
          .KKLAPPLVTLLSGEPEVQYVALRN.NLIVQKRPEILKQE.IKVFFVKYNDPIYVKLEKLDIMIRLASQA
Retrocopy PKKLAPPLVTLLSGEPEVQYVALRNFNLIVQKRPEILKQE>IKVFFVKYNDPIYVKLEKLDIMIRLASQA

Parental  NIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR
          NIAQVLAELKEYATEVDVDFVRKAV.AIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR
Retrocopy NIAQVLAELKEYATEVDVDFVRKAVQAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR

Parental  KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQ
          KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGE.AERIDNADELLESFLEGFHDESTQ
Retrocopy KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEFAERIDNADELLESFLEGFHDESTQ

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_2310 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020316	1 retrocopy	retro_btau_1675,
Choloepus hoffmanni	ENSCHOG00000010864	1 retrocopy	retro_chof_2310 ,
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mustela putorius furo	ENSMPUG00000014910	1 retrocopy	retro_mputfur_704,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925, retro_nleu_2554,