RetrogeneDB ID: retro_shar_195

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834609.1:4258189..4259062(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009835
• Aliases: None
• Description: None

Sequence

>retro_shar_195
CCCATGATTGAAGAGATTGACTCTTCAGATCAAAAAAGGAGAAGATACACTCCTTTTGATCTGGAAAAAATTAAGGATTT
GAAAAAAGGTTGCACTTTTTAAAGGGCTACATCATCTTATGTTAAGATGTTACTAGATAATTTGTCTTATAAAATCCTAA
CCCCCAATGTTTGGAAATCCATAGCAAGGACATGTTTAGAACCTGGACAAAACTTCCTGTGGCTTTCGGAGTATCATGAA
TTATGTAGGATTCAAGCCAGATACAATAGGCAAACGGGAGTTAATATACAAATCACTTTTGACCAACTAGTCAGTGAAGG
TCAGTATGGAGAAAATTCAGAACAGATTAATTACCCCATAACAGCTAATGAACAGATAGCCACTGCTACAACAAAAGTTT
GGGGTTCCCTCCCCAGACAAAAAGATTGACGGAAAGCCTTCACAAAAACAGAGCAAGGTCCCAATGAACCAACCCTTTGC
GGATTTTGTGGGATGTTTGCAGACAGCTGTCACAAGAACCATTGGAGAAAATGCAGCTACAGAAATAATGGCCATCTGGC
TAAGGAAAATGCTAATGAGGTTTGCACAAGAATTATATGGGGACTACACAAAGATGCTCCTTTAAAGGAGATCATAAGAT
GCTGTGCCACAGTGGACACAAATGCTTATTATACTCAGACTATGATGAACATAGGAAGACAGAGTCCCTCTTGGCAAAGG
ACTTCTAGAGAAACTCGTCAGTGCCTTCAGTGTGGAAAAGTTGGACATTTGAGAGCCCATTGTAGATATGGAGATAGAGT
GAGAAGACAAGGTGAGAGAATAAAACCCAAAACCCCATGTCCAAAATGCAACCAAGGCTTCCAGTGGGCCTCA

Alignment

ORF - retro_shar_195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.36 %
• Parental protein coverage: 87.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVVEKLNSSGQERRRYTPFNLEIIKDLKKACILYEATSSYVKMLLQNLAYEILTPSDWKSIARTCLGPGQ
          P..E...SS.Q.RRRYTPF.LE.IKDLKK.C....ATSSYVKMLL.NL.Y.ILTP..WKSIARTCL.PGQ
Retrocopy PMIEEIDSSDQKRRRYTPFDLEKIKDLKKGCTF*RATSSYVKMLLDNLSYKILTPNVWKSIARTCLEPGQ

Parental  NLLWLSEHSELCRIQIQQNKQTGVNTPITYDQLTGVSSYADISAQINYPIAAFQEIASAAIEAWGFLPGN
          N.LWLSE..ELCRIQ...N.QTGVN..IT.DQL.....Y...S.QINYPI.A...IA.A....WG.LP..
Retrocopy NFLWLSEYHELCRIQARYNRQTGVNIQITFDQLVSEGQYGENSEQINYPITANEQIATATTKVWGSLPRQ

Parental  KTDEKP-SKIEQGPNEP-FADFVGPLQTAIGENAAKEIMIRQ---LAKENANEVCRRIILGLCKDAPLEE
          K...K...K.EQGPNEP....F.G........N.......R....LAKENANEVC.RII.GL.KDAPL.E
Retrocopy KD*RKAFTKTEQGPNEPTLCGFCGMFADSCHKNHWRKCSYRNNGHLAKENANEVCTRIIWGLHKDAPLKE

Parental  IIRRCATVGTNTFYAQAMMQTS-QDPN-QGTSRETRQCFQCGKVGHLKGQCWHKDRAQQSGDN-HPDSDS
          IIR.CATV.TN..Y.Q.MM....Q.P..Q.TSRETRQC.QCGKVGHL...C...DR....G....P....
Retrocopy IIRCCATVDTNAYYTQTMMNIGRQSPSWQRTSRETRQCLQCGKVGHLRAHCRYGDRVRRQGERIKPKTPC

Parental  KQQNPGIFWTA
          ...N.G..W..
Retrocopy PKCNQGFQWAS

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_195 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009835	3 retrocopies	retro_shar_151, retro_shar_195 , retro_shar_429,
Sarcophilus harrisii	ENSSHAG00000016712	2 retrocopies	retro_shar_169, retro_shar_562,