RetrogeneDB ID: retro_shar_708

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861565.1:622171..622713(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000001503
• Aliases: None
• Description: None

Sequence

>retro_shar_708
AAGTCTTTAAATGCCAGAAGGAAAATTCTTATTCTAGCCATTGTTACTCCCATACAGAGCAATATTCAAAAAGAAGAGGG
CCACAGTTTGGTCAAATCTACATTAGCTGTCCATGATAAAATCAATTTCTTGATGAACAGTGGAGAAGGCCAATTCTTAT
CTCCTACTGAATTGGTTATTTCGAAGGGATGGAATGCTGTGGTTAAAGCTAGCCTGACTGCACTATCAGCCTTTGCAAAG
CAGTTTATAAGCCCTAGATAAAGAAACATGGATGGTCTATTATGAATATCATTACCATGTTAGATAGTAGATTTCCTAAT
TCCACACACAGTGGAACAGCAAGAGCTGGTGTTGAAAATATAAGCAAAACTTTGCCAATAGAATGCCACTGCAATGAAAT
AAGAATCAATTGTATTAGTCCTGATGTAATTTATTCTGCAACAGCCTTCAAGCAATCACAAAACCTTTGAAAAGGCATTA
AAGGATTCTTCCAACATTGTGTAACTAAGAGATTTGGTGTTCCTAAGGAAATTTCTTCCATC

Alignment

ORF - retro_shar_708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.98 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EELNAARQPSNPAIITPIQCNIRNEEEVNNLVKSTLDIHGKINFLVNNGGGQFLSLAELITSKGWKAVVE
          ..LNA.R.....AI.TPIQ.NI..EE....LVKSTL..H.KINFL.N.G.GQFLS..EL..SKGW.AVV.
Retrocopy KSLNARRKILILAIVTPIQSNIQKEEG-HSLVKSTLAVHDKINFLMNSGEGQFLSPTELVISKGWNAVVK

Parental  TNLTG-TFYLCKAVYNSWMKEHGGSMVNIIVTLTKGLPYASHSGAARAGVENLTKSLAIEWASHGVRINC
          ..LT..T..LCKAVY....K.HG.S..NII..L....P...HSG.ARAGVEN..K.L.IE......RINC
Retrocopy ASLTA<TISLCKAVYKP*IKKHGWSIMNIITMLDSRFPNSTHSGTARAGVENISKTLPIECHCNEIRINC

Parental  ISPGIIYSPTAFKNYENTTETNIKQYYQYCLAKRFGVPEEISSV
          ISP..IYS.TAFK...N.....IK...Q.C..KRFGVP.EISS.
Retrocopy ISPDVIYSATAFKQSQNL*K-GIKGFFQHCVTKRFGVPKEISSI

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_708 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014368	4 retrocopies	retro_cfam_1199, retro_cfam_1212, retro_cfam_1273, retro_cfam_568,
Sarcophilus harrisii	ENSSHAG00000001503	1 retrocopy	retro_shar_708 ,