RetrogeneDB ID: retro_shar_488

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849660.1:2470190..2470638(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX24
• Ensembl ID: ENSSHAG00000011329
• Aliases: None
• Description: sorting nexin 24 [Source:HGNC Symbol;Acc:21533]

Sequence

>retro_shar_488
GTCTTTAAGATAGAAATGCTAATGAGTAGACAGAATTATATTGTAGAAAACATTTAGAGTGAATTTCGGGCTCTGCATGA
AAAACCGAAGAAATGAATAAAAACTACAGAAATTTCTTCCAAACATGTTAGAAACTGGGTCCCCAAAGTCTTGGAACAGT
GACGATAAGGTCTGGAAGTCTATTTACAAGTTTTATTTTGGAAAATGAGGCGCTTTGGGAGTTATTTCCTGATTTTCTAA
ATGTACAACATTTACCCTTTCTACCAAAGATAGAAAGATTGTATCTCTTTTGAGGAAACAGAATTTTAAAAGTCTAGCAA
ACGACCTTACCAGTCAGTGCTGCTGTTCCTAAGGAATCCACATGTCTTGCCCTAAAACCAATGAAGATTTTCCAAAAGTA
GTTATTGGAGTTGTCCTTGGGATATTTTACCCTCATCTACAGCCCAAG

Alignment

ORF - retro_shar_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 76.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFKIEVLMSGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLEAYLQAV-ILEN
          VFKIE.LMS.....VE...SEF.ALH.K.KK.IKT.EI.SKHVRNWVPKVLEQ.R.GLE.YLQ...ILEN
Retrocopy VFKIEMLMSRQNYIVENI*SEFRALHEKPKK*IKTTEISSKHVRNWVPKVLEQ*R*GLEVYLQVL<ILEN

Parental  EELPKLFLDFLNIRHLPSLPKTE-SCGSFEETESEESSKLSHQPVLLFLRDPYVL-PTANDHFPNVVIEG
          E.L..LF.DFLN..HLP.LPK.E..C.SFEETE...SSK...Q.VLLFLR.P.VL.P..N..FP.VVI.G
Retrocopy EALWELFPDFLNVQHLPFLPKIE>DCISFEETEF*KSSKRPYQSVLLFLRNPHVL>PKTNEDFPKVVI-G

Parental  VLHGIFYPHLQPR
          V..GIFYPHLQP.
Retrocopy VVLGIFYPHLQPK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_488 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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,