RetrogeneDB ID: retro_shar_430

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842525.1:111547..112126(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX7
• Ensembl ID: ENSSHAG00000014440
• Aliases: None
• Description: syntaxin 7 [Source:HGNC Symbol;Acc:11442]

Sequence

>retro_shar_430
GATCAGTACATAAAAGATTTTGGACCTTTGCCCACCACTCCAAGTAAGTAGTATCAAAGGAAAATATAGAAATATAAGCT
CATTGCTGAATTCACAGCTTCACTAACAAACTGCAAGAAGGTCCAAAGACAAGTTGCTGAAAGAGTTTGTTGCCAAAGTA
AGAGCAAGTTCCAGGTCTCTAGTTGTTTTCCTGAGGTGGTCCTAAAGAGAATGATCTTATATCATGGCCAAGTGAAACCC
AATCTCAAGCATGGCTGCAGGATGAAGACACTGCAGAAGGTGAATTACATCTTATTCTAGAGAGAGAATCTTCCATTAGG
CAACTTGAAGCTGATAGAACAATTATAAATGAAATATTTAAGGAGTTAGCTGTGAAGATTCATCAACAAAGAGATGTGAT
AGATAGCATAAAAGCCAATATAGATGACATCAAAGTACATATCCAGCAGGCAAACAAGCAGCTATCTAGGACTGCAAATT
ATCAGTGCAAGTCCTAAAACTGTGTACATTATTCTTTTGATTGTTGTTATTAGATTGATGACTGTTGGGCTTATCATTGG
GAGATCCTTCAAAAAAAGT

Alignment

ORF - retro_shar_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.8 %
• Parental protein coverage: 74.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKYIKEFGSLPTTPSEQRQRKIQKDRLVAEFTASLTNFQKVQRQAAEKEKDFVARVRASSRVSGGFPE-D
          D.YIK.FG.LPTTPS...QRKI.K..L.AEFTASLTN..KVQRQ.AE..............VS..FPE..
Retrocopy DQYIKDFGPLPTTPSK*YQRKI*KYKLIAEFTASLTNCKKVQRQVAER---VCCQSKSKFQVSSCFPE<G

Parental  SSKERNLVSWESQTQPQAQLQDEDITEDDLHLIQERESSIRQLEADIMDINEIFKDLGMMIHEQGDVIDS
          ..KE..L.SW.S.TQ.QA.LQDED..E..LHLI.ERESSIRQLEAD...INEIFK.L...IH.Q.DVIDS
Retrocopy GPKENDLISWPSETQSQAWLQDEDTAEGELHLILERESSIRQLEADRTIINEIFKELAVKIHQQRDVIDS

Parental  IEANVENAEVHIQQANQQLSRAADYQRKS-RKTLCIILFIVVIGLVILGLILWGSLKKS
          I.AN.....VHIQQAN.QLSR.A.YQ.KS......I.L.IVVI.L...GLI...S.KKS
Retrocopy IKANIDDIKVHIQQANKQLSRTANYQCKS>KTVYIILL-IVVIRLMTVGLIIGRSFKKS

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_430 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010117	3 retrocopies	retro_chof_1503, retro_chof_2631, retro_chof_829,
Dasypus novemcinctus	ENSDNOG00000000295	1 retrocopy	retro_dnov_600,
Felis catus	ENSFCAG00000002292	1 retrocopy	retro_fcat_977,
Myotis lucifugus	ENSMLUG00000004301	1 retrocopy	retro_mluc_494,
Sarcophilus harrisii	ENSSHAG00000014440	1 retrocopy	retro_shar_430 ,
Tursiops truncatus	ENSTTRG00000009853	1 retrocopy	retro_ttru_185,