RetrogeneDB ID: retro_shar_118

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867745.1:12510..13281(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000001527
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000018446
• Aliases: None
• Description: None

Sequence

>retro_shar_118
ATGGGCAAGCCACCCTCCCAGGCGCCCGGTTTGCTGCCCGAGGACTCTCTCATCGAAGGAGTCAGCGACCAGGTGCTCGT
GGCCGTGCTCTTCGGCTGCGCTTTCCTGGTGGTGGTGGGCTACGTGCTCCTCAGAAACGCCCGGCAGCACATCCATCCCA
ACAACCGCGAGCTCGTCCGGGTGGTGAGAGAGCAACTCCACCGGGAGCAGGATCCTCCGGCCCCTCGCCCTCAGTTCTAC
ACGGACCTGTCCTGCCCCATCTGTTTACATCACGCCTCTCTTCCCATCGAGACCAACTGTGGCCACCTCTTCTGCGGCAA
CTGCCTCATCGCTTACTGGCGCTACGGCTCGTGGCTCGGGATGGTCAGCTGTCCCATCTGTCGCCAAACGGTGACTTTGC
TGTTCCCCGTGTTCGCCGAAGACGTGCACTCCGTCGAAGCCCGGCGTTTGCATCAGGATATCCACGACTACAACCGAAGG
TTCTCGGGACAGCCCCGGTCCGTTATGGACAGACTTCTGGATCTCCCCACTCTGCTGAGACACGCCTTCCGAGAAGTGTT
CTCCGTGGGAGGACTTTTCTGGATGTTTCGCATCAGGATCGTCCTGTGTCTGGTGGGAGCCTTTTTCTACCTGATATCCC
CTTTGGATTTGGTTCCCGAAGGCTTATTTGGGATTCTGGGGTTTCTGGACGATTTCTTTGTCATCTTTCTCTTGCTTATT
TACATCTCTATCATGTATAGGGAAGTAATAACACAGAGGCTGAACAGATGA

Alignment

ORF - retro_shar_118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKHQSGIQSLKLDDSIIEGVSDQVLVAVVISFAFIATLIYILLRNAEQNIHPDNQELVRVLREQLQTDQ
          M.K..S....L...DS.IEGVSDQVLVAV....AF.....Y.LLRNA.Q.IHP.N.ELVRV.REQL...Q
Retrocopy MGKPPSQAPGLLPEDSLIEGVSDQVLVAVLFGCAFLVVVGYVLLRNARQHIHPNNRELVRVVREQLHREQ

Parental  QDAPAVVRQQFYTDMSCPICLHQASLPIETNCGHLFCGTCIIAYWRYGSWLGAISCPICRQTVTLLLPVF
          ...P...R.QFYTD.SCPICLH.ASLPIETNCGHLFCG.C.IAYWRYGSWLG..SCPICRQTVTLL.PVF
Retrocopy D--PPAPRPQFYTDLSCPICLHHASLPIETNCGHLFCGNCLIAYWRYGSWLGMVSCPICRQTVTLLFPVF

Parental  SEDNQTQDVSELHQDINDYNRRFSGQPRSILERIMDLPTLLRHAFREMFSVGGLFWMFRIRILLCLLGAF
          .ED........LHQDI.DYNRRFSGQPRS...R..DLPTLLRHAFRE.FSVGGLFWMFRIRI.LCL.GAF
Retrocopy AEDVHSVEARRLHQDIHDYNRRFSGQPRSVMDRLLDLPTLLRHAFREVFSVGGLFWMFRIRIVLCLVGAF

Parental  FYLISPLDFVPEALFGILGFLDDFFVIFLLLIYISIMYREVLTQRLNR
          FYLISPLD.VPE.LFGILGFLDDFFVIFLLLIYISIMYREV.TQRLNR
Retrocopy FYLISPLDLVPEGLFGILGFLDDFFVIFLLLIYISIMYREVITQRLNR

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_118 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001127	1 retrocopy	retro_meug_862,
Monodelphis domestica	ENSMODG00000010090	1 retrocopy	retro_mdom_197,
Mus musculus	ENSMUSG00000013878	1 retrocopy	retro_mmus_2907,
Otolemur garnettii	ENSOGAG00000007925	1 retrocopy	retro_ogar_2905,
Pteropus vampyrus	ENSPVAG00000013497	1 retrocopy	retro_pvam_856,
Sorex araneus	ENSSARG00000006471	1 retrocopy	retro_sara_706,
Sarcophilus harrisii	ENSSHAG00000018446	1 retrocopy	retro_shar_118 ,