RetrogeneDB ID: retro_chof_544

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_119732:2217..2550(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX24
• Ensembl ID: ENSCHOG00000006859
• Aliases: None
• Description: sorting nexin 24 [Source:HGNC Symbol;Acc:21533]

Sequence

>retro_chof_544
CCAGAAATCCTCTCTAAACATGTGAGAATCTGGGTTCTGAAAGTCCTGGAATGATGACAAGGTTTGGAACCATATTTAAA
GGTTTTCATTTTAGAAAACAAAGAACTCCCCAAACTATTTCTTGATTTCCCAAACACATGACAATTGCCTTCTCTACCAA
AAGGCAGAGAGTTGTGGATCTTTTAATGAGACAGAATCTGAAGAGTCAAACAGTCCCATCAGCCAGTGCTGCTGTTCCTT
GGGTACCCATATGTCTTCACTACAGCTAACAATTTTCCAAATGTGATTACTGAAGTTCTCCATGAGATATTTTCCCCTCC
CCTGTGGCCCAGG

Alignment

ORF - retro_chof_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.52 %
• Parental protein coverage: 57.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHLPSLPK-TESCGSFDETESEE
          PEI.SKHVR.WV.KVL....QGLE.YL...ILEN.ELPKLFLDF.N...LPSLPK..ESCGSF.ETES.E
Retrocopy PEILSKHVRIWVLKVL-E**QGLEPYLKVFILENKELPKLFLDFPNT*QLPSLPK>AESCGSFNETES-E

Parental  SS-RLSHQPVLLFLRDPYVLPAASXXPNVVMEGVLHGIFYSQLQPR
          .S...SHQPVLLFL..PYV...A...PNV..E.VLH.IF...L.PR
Retrocopy ES<KQSHQPVLLFLGYPYVFTTANNFPNVITE-VLHEIFSPPLWPR

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_544 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031069	1 retrocopy	retro_btau_640,
Choloepus hoffmanni	ENSCHOG00000006859	2 retrocopies	retro_chof_1841, retro_chof_544 ,
Dasypus novemcinctus	ENSDNOG00000019810	1 retrocopy	retro_dnov_261,
Echinops telfairi	ENSETEG00000010310	1 retrocopy	retro_etel_923,
Microcebus murinus	ENSMICG00000001708	1 retrocopy	retro_mmur_1043,
Myotis lucifugus	ENSMLUG00000009392	2 retrocopies	retro_mluc_1022, retro_mluc_2330,
Monodelphis domestica	ENSMODG00000013427	1 retrocopy	retro_mdom_1215,
Otolemur garnettii	ENSOGAG00000005170	2 retrocopies	retro_ogar_2940, retro_ogar_975,
Sorex araneus	ENSSARG00000009785	1 retrocopy	retro_sara_99,
Sarcophilus harrisii	ENSSHAG00000011329	1 retrocopy	retro_shar_488,
Tarsius syrichta	ENSTSYG00000014395	2 retrocopies	retro_tsyr_1563, retro_tsyr_1691,