RetrogeneDB ID: retro_shar_189

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834594.1:282650..283181(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11B
• Ensembl ID: ENSSHAG00000006816
• Aliases: None
• Description: RAB11B, member RAS oncogene family [Source:HGNC Symbol;Acc:9761]

Sequence

>retro_shar_189
GTAGGGAAGAGCAATCTCCTTTCATGATTCACTCGAAACGAACTCAGTTTGGAGAGTAAAAGTACCATCCGTGTGGAATT
TGCAACCAGGAGCATCCAGGTGGAGAGGAAGACTGTAAAAGCCAAATCTGGGTCACAGCTGGTCAGGAGCAGTACCTGCA
ATCACATCAGCGTACTACCGAGGGACTGTGGGAGCCCTGTTGGTCTATGACATTGCCAAGCACCTGACATATGAGGATGT
GGAACGCTGACTGAAAGAACTCCGTGATCATGCTGACAACAACATTGTCATCACACTGGCGGGGAACAAGAGTGACCTGC
GGGCATACTGTGCCCACTAATGAGGACGGGCATTCGCAGAGAAAAACTATTTGTTTTTTATTGAGATGTCAGCCTTGGAT
TCAACCAATGTGGAAGAAGCCTTTAAGAACATTCTCACAGAGATTTACGACATGGTATCCCAAAGCAGATTGCTGACCAC
TCTGCACATGATGAATCTCCTGACAACAATGTGATAGACATCAGCATCCCC

Alignment

ORF - retro_shar_189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.38 %
• Parental protein coverage: 82.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKA-QIWDTAGQERYR-AITSAYYRGAVGALL
          VGKSNLLS.FTRNE..LESKSTI.VEFATRSIQV..KT.KA.QIW.TAGQE.Y..AITSAYYRG.VGALL
Retrocopy VGKSNLLS*FTRNELSLESKSTIRVEFATRSIQVERKTVKA<QIWVTAGQEQYL<AITSAYYRGTVGALL

Parental  VYDIAKHLTYENVERWLKELRDHADNNIVIMLV-GNKSDLRHLRAVPTDE-ARAFAEKNNLSFIETSALD
          VYDIAKHLTYE.VER.LKELRDHADNNIVI.L..G......H...VPT.E..RAFAEKN.L.FIE.SALD
Retrocopy VYDIAKHLTYEDVER*LKELRDHADNNIVITLA>GTRVTCGH--TVPTNE<GRAFAEKNYLFFIEMSALD

Parental  STNVEEAFKNILTEIYRIVSQ-KQIADRSAHDESPGNNVVDISVP
          STNVEEAFKNILTEIY..VSQ.KQIAD.SAHDESP.NNV.DIS.P
Retrocopy STNVEEAFKNILTEIYDMVSQ<KQIADHSAHDESPDNNVIDISIP

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_189 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Sarcophilus harrisii	ENSSHAG00000006816	1 retrocopy	retro_shar_189 ,
Sarcophilus harrisii	ENSSHAG00000017800	1 retrocopy	retro_shar_80,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,