RetrogeneDB ID: retro_chof_2306

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_64730:9498..10215(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC57
• Ensembl ID: ENSCHOG00000006482
• Aliases: None
• Description: leucine rich repeat containing 57 [Source:HGNC Symbol;Acc:26719]

Sequence

>retro_chof_2306
ATGGGGAACAGTGCCCTCCGCGCTCATGTGGAAACAGCGCAGAAAACGGGTGTCTTTGAGCTCAAGGACCGCGGACTGAC
CGAGTTCCCTTCAGAGTTGCAGAAGCTGACGAGCAATCTCAGGACCATCGACTTATCCAACAACAAGATCCAGAGCCTAC
CGCCTATGCTGATAGGGAAGTTCACTCTGCTGAAGAGCCTCTCCCTGAACAACAACAAACTGACTCTTCTGACTGATGAG
TTATGCAATCTGAAAAAACTAGAGATGCTAAGCCTAAACAACAATCACCTGATGGATTTGCCATCTACCTTTGGACACCT
CTCAGCCCTCAAGACCCTGAGCCTCTCTGGGAACCAACTCCGGACACTACCACCCCAACTCTGTAGCCTACGGCACCTGG
ATGTTGTGGATCTCTCTAAGAACCAGATTCGGAGTATACCTGACATAGTGGGAGAGCTGCAGGTCATCGAACTCAACCTC
AATCAGAACCAGATATCTCAGATCTCAGTGAAGATATCTTGCTGTCCTCGCCTCAAAGTTCTTCGCCTGGAAGAGAACTG
TCTTGAGCTCAGTATGCTTCCACAGAGTATCCTCAGTGATTCCCAGATCTGTCTGCTTGCTGTGGAAGGCAATCTTTTTG
AGATAAAGAACCTTCGAGAACTGGAAGGCTATGATAAGTACATGGAGAGGTTTACAGCTACCAAGAAGAAGTTTGCA

Alignment

ORF - retro_chof_2306 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNSALRAHVETAQKTGVFQLKDRGLTEFPSELQKLTSNLRTIDLSNNKIESLPPLLIGKFTLLKSLSLN
          MGNSALRAHVETAQKTGVF.LKDRGLTEFPSELQKLTSNLRTIDLSNNKI.SLPP.LIGKFTLLKSLSLN
Retrocopy MGNSALRAHVETAQKTGVFELKDRGLTEFPSELQKLTSNLRTIDLSNNKIQSLPPMLIGKFTLLKSLSLN

Parental  NNKLTLLPDELCNLKKLEMLSLNNNHLMDLPSTFGHLSALKTLSLSGNQLRTLPPQLCSLRHLDVVDLSK
          NNKLTLL.DELCNLKKLEMLSLNNNHLMDLPSTFGHLSALKTLSLSGNQLRTLPPQLCSLRHLDVVDLSK
Retrocopy NNKLTLLTDELCNLKKLEMLSLNNNHLMDLPSTFGHLSALKTLSLSGNQLRTLPPQLCSLRHLDVVDLSK

Parental  NQIRSIPDIVGELQVIELNLNQNQISQISVKISCCPRLKVLRLEENCLELSMLPQSILSDSQICLLAVEG
          NQIRSIPDIVGELQVIELNLNQNQISQISVKISCCPRLKVLRLEENCLELSMLPQSILSDSQICLLAVEG
Retrocopy NQIRSIPDIVGELQVIELNLNQNQISQISVKISCCPRLKVLRLEENCLELSMLPQSILSDSQICLLAVEG

Parental  NLFEIKNLRELEGYDKYMERFTATKKKFA
          NLFEIKNLRELEGYDKYMERFTATKKKFA
Retrocopy NLFEIKNLRELEGYDKYMERFTATKKKFA

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_2306 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306 ,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,