RetrogeneDB ID: retro_shar_761

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864154.1:820..1427(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM19
• Ensembl ID: ENSSHAG00000001776
• Aliases: None
• Description: transmembrane protein 19 [Source:HGNC Symbol;Acc:25605]

Sequence

>retro_shar_761
ATTCAAGTTTTCGGTAATGGAGCTGTACCTACAGAGCTGGCATTGCTCTGTATGACTGAAAATGGGCCAGGTGAAATCTG
CCTTGATTTCTTCAGACAATACATTACTTCCTGGATGTGTTTGTGTCTCTTGACTTCCTTGAGTTTTTTTGCAGGAGATA
CATAGTCTTCTGAAATTGGCTCTGTTGCAAGTACTACCCAACCAATGCTGATAACAACCTGACAAAGAGTTCCTATTGGT
ATCAATACAGGGGTCACTATGGTAGGCTTTCTCTCCAGCTTTCCTGGTGAGTCTTTAATGAAAACTGCCTACTTCTTCTT
CTTACAGCCGATTTTTGTGAATGATATGGAATCTTTTCCCCAATGACCAGTTGTTGCATTTGCAGGAAGGGCTGGTTTAT
AGAGATCAGTTATTGATTCATACTTAGAAGCAACAATGCAGTACTCTGGTTGGGATGAAAGCACCTACACAGTTGTCAGC
CAGCCAACTGGTGAGACAAAATACACATTGAGGAAACCTATTCTTGATAACAATGCTGTGAACTTTTTCTTTAATTCTCA
TTGCTCTCTTGCTTCCTAGTGCACAATGGCCTCTCTGGCCCATAGAC

Alignment

ORF - retro_shar_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.12 %
• Parental protein coverage: 59.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQVFCNGAVPTELALLYMIENGPGEICIDFSRQYTASWMCLSLLASLASSAGDTWASEIGSVASTTQPRL
          IQVF.NGAVPTELALL.M.ENGPGEIC.DF.RQY..SWMCL.LL.SL...AGDT..SEIGSVASTTQP.L
Retrocopy IQVFGNGAVPTELALLCMTENGPGEICLDFFRQYITSWMCLCLLTSLSFFAGDT*SSEIGSVASTTQPML

Parental  ITTWQRVPIGTNGGVTAVGFLSSFLGGSLVGIAY-FFSQLIFVNDLESSAPQWPVVAFAGMAGLLGSVID
          ITT.QRVPIG.N.GVT.VGFLSSF.G.SL...AY.FF.Q.IFVND.E.S.PQ.PVVAFAG.AGL..SVID
Retrocopy ITT*QRVPIGINTGVTMVGFLSSFPGESLMKTAYFFFLQPIFVNDME-SFPQ*PVVAFAGRAGL*RSVID

Parental  SYLGATMQYSGWDESTHTVVSQPTGETKYISGKPILDNNAVNLFSS-ILIALLLPSAAWALWPIE
          SYL.ATMQYSGWDEST.TVVSQPTGETKY...KPILDNNAVN.F.......LL.PSA.W.LWPI.
Retrocopy SYLEATMQYSGWDESTYTVVSQPTGETKYTLRKPILDNNAVNFFFN>LIALLL-PSAQWPLWPID

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_761 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
Oryctolagus cuniculus	ENSOCUG00000012539	1 retrocopy	retro_ocun_876,
Sarcophilus harrisii	ENSSHAG00000001776	1 retrocopy	retro_shar_761 ,