RetrogeneDB ID: retro_shar_229

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834719.1:113437..113714(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSTB
• Ensembl ID: ENSSHAG00000017952
• Aliases: None
• Description: cystatin B (stefin B) [Source:HGNC Symbol;Acc:2482]

Sequence

>retro_shar_229
ATGTATGGACGAATTTCAACTGCTAAAATTGCCATGGCTGAAATGAAGCAGACCATGGATGAGGTAAAAACACAGCTTGA
AGAGAAAGAAAAATAGAAAGTTTCCCATCTTTAAGATTATGGAATTTAAAAGTCAAGCGATTGCTGGGACAAACTACTTT
ATTAAGGCTCACCTTGATGAAGAGGAATTTATACATATTCAAATGTACAAAAGTTTCCCTCATGAAAACAGGCCATTGGT
TCTATCCAATTATCAAACCTACAAAACCAGGTCGGAC

Alignment

ORF - retro_shar_229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.52 %
• Parental protein coverage: 88.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCGGTSATKPATAETQRIADEVKTQLEAKE-NRKFPVFKTMEFKSQVVAGTNYFIKVHVGEEEFIHMRVF
          M.G..S..K.A.AE.....DEVKTQLE.KE.NRKFP.FK.MEFKSQ..AGTNYFIK.H..EEEFIH....
Retrocopy MYGRISTAKIAMAEMKQTMDEVKTQLEEKE>NRKFPIFKIMEFKSQAIAGTNYFIKAHLDEEEFIHIQMY

Parental  ESLPHENKPLLLSSYQTNKTKDD
          .S.PHEN.PL.LS.YQT.KT..D
Retrocopy KSFPHENRPLVLSNYQTYKTRSD

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_229 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000524	1 retrocopy	retro_btau_97,
Loxodonta africana	ENSLAFG00000002664	1 retrocopy	retro_lafr_370,
Myotis lucifugus	ENSMLUG00000022457	1 retrocopy	retro_mluc_379,
Macaca mulatta	ENSMMUG00000012303	1 retrocopy	retro_mmul_1609,
Otolemur garnettii	ENSOGAG00000006101	2 retrocopies	retro_ogar_3274, retro_ogar_3275,
Pteropus vampyrus	ENSPVAG00000007022	1 retrocopy	retro_pvam_1089,
Rattus norvegicus	ENSRNOG00000001201	1 retrocopy	retro_rnor_551,
Sarcophilus harrisii	ENSSHAG00000017952	3 retrocopies	retro_shar_229 , retro_shar_623, retro_shar_699,