RetrogeneDB ID: retro_shar_641

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856902.1:2448294..2449082(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC61A1
• Ensembl ID: ENSSHAG00000013915
• Aliases: None
• Description: Sec61 alpha 1 subunit (S. cerevisiae) [Source:HGNC Symbol;Acc:18276]

Sequence

>retro_shar_641
GAGTCTACAAAAGACTACAATCTATTAAAGGGACCTCAGAAGTTATTTGTTATGATTTTATCATTGGGCAAACCATTGTG
TGTGTGTGATGACTGGGATGTATGGAGATCATAATGAATTAAGTTCTGAAGTTTTTCTACTTAGTCAATCAATTTTCTGT
TGTTTCTTTGATTGTACTGCTGTCAGATGAACTTTTACAGGATGGTTACAACTCAGAGTTGGGTATTTCATTTTTAATTG
CTACTAATATATGTCAAACCATCATCCTGATGGTGTTTAGCCCCACTGCCATTAACGCTGGTAAAAGAACTGAGTTTGAG
GGTTCAATCATTGCTCCATTTCACTTATTGGTTAACAGAATAGACAAAACTCATATTCAAGAAGCCTTCCATCCATCACC
ATATTTCGCTCAGTCTCATGAAACCCATTGTTACATTCTTTGTGTTTGCTATTATTATATACCTTCAGGAATTTCATGTC
AATTTACCCATCAAGTCTGCTCAAAATTATACACAATACAGTAGTTATCCCATCAAGCTCTTCTCCAGTTTCAACATTCC
TATCATTCTTCAATCTGTCCTGTTTCTATATGTTATATTCCAGACGTCATTTGTCCAGTTTAGTGGCCACTTTTTATTTT
TATTAGAATAATGGTCTGATGGAATTGCAAAAGGTCCTGCATGTTACTACTTAATTAAAGTCCTATGTTAGTATGTTTCT
CCTCCAGAATATAAAAGTGCCATATTTGAAAATCCTGTCCATATTGTTTTCACATAATCTTTATGCTG

Alignment

ORF - retro_shar_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.74 %
• Parental protein coverage: 55.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DTPKDRALFNGAQKLFGMIITIGQSI-VYVMTGMYGDPSEMGAGICLLITIQLF-VAGLIVLLLDELLQK
          ...KD..L..G.QKLF.MI...G....V.VMTGMYGD..E.......L.....F.V..LIVLL.DELLQ.
Retrocopy ESTKDYNLLKGPQKLFVMILSLGKPL>VCVMTGMYGDHNELSSEV-FLLSQSIF>VVSLIVLLSDELLQD

Parental  GYGLGSGISLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTD-KVRALREAFYRQNLP
          GY....GIS..IATNIC.TI....FSPT..N.G...EFEG.IIA.FHLL..R.D.K..............
Retrocopy GYNSELGISFLIATNICQTIILMVFSPTAINAGKRTEFEGSIIAPFHLLVNRID>KLIFKKPSIHHHISL

Parental  NLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLYVISQMLSA
          .LM..I.T.FVFA..IY.Q.F.V.LPIKSA....QY..YPIKLF...NIPIILQS.L...LYVI.Q....
Retrocopy SLMKPIVTFFVFAIIIYLQEFHVNLPIKSAQNYTQYSSYPIKLFSSFNIPIILQSVLF--LYVIFQTSFV

Parental  RFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCYYLSPPESFGSVLEDPVHAV-VYIVFML
          .FSG..L..LL..WSD....GPA..Y....LC.Y.SPPE......E.PVH.V...I.FML
Retrocopy QFSGHFLF-LLE*WSDGIAKGPACYYLIKVLC*YVSPPEYKSAIFENPVHIV<FHIIFML

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_641 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015763	1 retrocopy	retro_dnov_2642,
Sarcophilus harrisii	ENSSHAG00000013915	1 retrocopy	retro_shar_641 ,