RetrogeneDB ID: retro_chof_1566

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_3270:33695..34220(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMMECR1L
• Ensembl ID: ENSCHOG00000009373
• Aliases: None
• Description: AMMECR1-like [Source:HGNC Symbol;Acc:28658]

Sequence

>retro_chof_1566
CCACTGTTTGTAACATGGAAGATCGGTCGAGACAAAAGATTGCGTGGATGCATAGGTACTTTTTCTGCCATGAATTTGCA
TTCAGGACTCAGGGAGTACACACTTACCAGTGCCCTTAAAGATAGCCGTTTTCCCCCAATGACAAGGGATGAGCTGCCGC
GGCTTTTCTGCTCAGTGTCTTTGCTCACTAACTTTGAAGATGTCTGTGATTATTTGGACTGGGAGGTGGGTGTACATGGC
ATTAGAATAGAATTCATCAATGAAAAAGGATCAAAACGCACCGCCACCTACCTACCGGAGGTTGCAAAGGAGCAAGGATG
GGACCATATTCAGACCATCGACTCTTTACTAAGGAAAGGAGGATACAAAGCTCCAATCACTAATGAATTCAGGAAAACCA
TAAAACTGACCAGGTACCGTAGTGAAAAGATGACCCTAAGCTATGCTGAATACCTTGCTCATCGCCAGCATCATCATTTC
CAAAACGGCATTGGTCATCCCCTTCCACCATACAACCATTATTCC

Alignment

ORF - retro_chof_1566 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLFVTWKTGRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFPPLTREELPKLFCSVSLLTNFEDASD
          PLFVTWK.GRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFPP.TR.ELP.LFCSVSLLTNFED..D
Retrocopy PLFVTWKIGRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFPPMTRDELPRLFCSVSLLTNFEDVCD

Parental  YLDWEVGVHGIRIEFINEKGVKRTATYLPEVAKEQDWDQIQTIDSLLKK-GFKAPITSEIRKTIKL-RYR
          YLDWEVGVHGIRIEFINEKG.KRTATYLPEVAKEQ.WD.IQTIDSLL.K.G.KAPIT.E.RKTIKL.RYR
Retrocopy YLDWEVGVHGIRIEFINEKGSKRTATYLPEVAKEQGWDHIQTIDSLLRKGGYKAPITNEFRKTIKLTRYR

Parental  SEKVTISYAEYIASRQ-HCFQNGTLHAPPLYNHYS
          SEK.T.SYAEY.A.RQ.H.FQNG..H..P.YNHYS
Retrocopy SEKMTLSYAEYLAHRQHHHFQNGIGHPLPPYNHYS

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_1566 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566 ,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86,