RetrogeneDB ID: retro_chof_691

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_135577:35..953(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM98A
• Ensembl ID: ENSCHOG00000000476
• Aliases: None
• Description: family with sequence similarity 98, member A [Source:HGNC Symbol;Acc:24520]

Sequence

>retro_chof_691
TATCAGGGACCACTGTTAGAAGAGCAAACCCTTGGCAAGGCGGCAGAGGGTGGACTATCTTCACCTGAATTTTCAGAGCT
CTGTGTTTGGTTAGGCTTTCAAATAAAATCATTGTGCGACTTGGAAGAAAGTATCACTTTAGCTGGGAAAGATCATCTAG
AAAGTTTCCAGCTTGAGATAAGTGGTTTTTTCAAAGAAATGCCATGTCCATTTTCTGTACTAATTTCAGGAGATATTAAA
GACTGTTTGAAAAAGAAGGAATACTGTTTGAAACTTCTATTATTTTTAAGTACAGAGCTTCAAGCTTTACAGATCTTACA
GAACAAGAAATGTAAAAATTCTCAGTTAGATAAAAATAGCGAAATTTATCAGGAAGTTCAAGCTATCAGTGATACCCTTG
GTGTACCCACGTCAACAACTTCTAACATTCCACTTATGCTAAACCAAGTGGAATCAAAGGTTAAGGATATCCTCTCAAAA
GTCCAGAAAAATCATGTGGGAAAACCACTGCTGAAAATTGACTTAAATCCGGAACAGGCGGAACAACTGGAAAGAATCAA
CGATGCTTTTTACTGTGAATATGAATGTCGTCGGTGGATGGTAATGAAACAATTAGATGTAACAGTGCAATCCTTTGGAT
GGTCCGATAGAGCAAACATAAAAGCAGATGACATAGCAAGAATTTACCAGCCTAAGCATTATGCTTTGTCACCCAAGACA
ACTATTACATTAGCACATCTACTTGCTGCTCATGAAGATCTATCCAAGATCATTAGAACAAGTAGCGGCGCTACCTGGGA
GAAGACAGCTTATGCCAGTAGCAAGTTGCTGATGGGAAGGGTGCCTGACACGGGAGGAAGGCCAAATGAAATTGAACCAC
CACCCCCTAAAATGCCCCCTTGGCAGAAGAGACAAGAA

Alignment

ORF - retro_chof_691 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.97 %
• Parental protein coverage: 62.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YKGPLLEDGALSQAVSSGASSPEFTKLCAWLVSELRVLCKLEENVQATNSPSEAEEFQLEVSGLLGEMNC
          Y.GPLLE...L..A...G.SSPEF..LC.WL......LC.LEE...........E.FQLE.SG...EM.C
Retrocopy YQGPLLEEQTLGKAAEGGLSSPEFSELCVWLGFQIKSLCDLEESITLAGK-DHLESFQLEISGFFKEMPC

Parental  PYLSLTSGDVTKRLLVQKNCLLLLTYLISELEAARMLCVNAPPKKAQEGGGSEVFQELKGICIALGMSKP
          P...L.SGD....L.....CL.LL..L..EL.A...L..N...K..Q....SE..QE...I...LG...P
Retrocopy PFSVLISGDIKDCLKKKEYCLKLLLFLSTELQALQIL-QNKKCKNSQLDKNSEIYQEVQAISDTLGV--P

Parental  PANITMFQFFSGIEKKKLKETLAKVPPNHVGKPLLKKPMGPAHWEKIEAINQAIANEYEVRRKLLIKRLD
          ................K.K..L.KV..NHVGKPLLK....P...E..E.IN.A...EYE.RR....K.LD
Retrocopy TSTTSNIPLMLNQVESKVKDILSKVQKNHVGKPLLKIDLNPEQAEQLERINDAFYCEYECRRWMVMKQLD

Parental  VTVQSFGWSDRAKSQTEKLAKVYQPKRSVLSPKSVISVAHLLAARQDLSKILRTSSGSIREKTACAINKV
          VTVQSFGWSDRA.......A..YQPK...LSPK..I..AHLLAA..DLSKI.RTSSG...EKTA.A..K.
Retrocopy VTVQSFGWSDRANIKADDIARIYQPKHYALSPKTTITLAHLLAAHEDLSKIIRTSSGATWEKTAYASSKL

Parental  LMGRVPDRGGRPNEIEPPPPEMPPWQKRQD
          LMGRVPD.GGRPNEIEPPPP.MPPWQKRQ.
Retrocopy LMGRVPDTGGRPNEIEPPPPKMPPWQKRQE

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_691 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005268	2 retrocopies	retro_amel_1607, retro_amel_1845,
Choloepus hoffmanni	ENSCHOG00000000476	1 retrocopy	retro_chof_691 ,
Mustela putorius furo	ENSMPUG00000010098	1 retrocopy	retro_mputfur_1193,
Rattus norvegicus	ENSRNOG00000030328	1 retrocopy	retro_rnor_614,