RetrogeneDB ID: retro_shar_569

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850091.1:64029..64653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011140
• Aliases: None
• Description: None

Sequence

>retro_shar_569
CTTTTTGGCAAAAAGGTGATTGGCAAATATCTAAAATTTTTAAGGATCAAATCACTGATTCTCTAAAACGAGGTGTTTAA
TACTTAATCAGGATTGGATAACCTCAACTTTATATCATCCAGCATCCTTTAGAAGAATTCAAAGATTGCCTAGCATTTGT
ATAGAACCAGTATGTGCAAGTTTAGTCAGTGTTCTTGGCAACTGGGAAAATCTGCCTTCAACAGAGTCCCTGACATTAAG
GATTATAAATTTTATGATGTAGAAACAAAATATGTGTGACTTCAGGTTTCTGAAAAATTGTCATTTTTACATAACAGCAT
CAAAATGGTGGTGAAAACCTCACTCCAGAAAATACAATATTGAATAAATAGGAGCCTGGAAAATAATTGACTTCGATTTT
TGGTCTACATCACTAAATTCTTCTAAAAAAAAGTCTAACTTCTCCTCTAAAGAGTAGGTTCAATATTTACTTTCCTTATA
CCTACAATATACTGAATATTTGCTCCTGAGCATATACTTTCTATGAATTGTGTTAAGTACTCTTTAGAAGTTGTTGTTTA
TTCTGTGTTTAATAAAGGAAAGCCTGTCTTTGAAATCAATAAGCAAGACATACATAAAAATTTC

Alignment

ORF - retro_shar_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 63.88 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VFDKKQIDKYQKFE-KDQIIDSLKRGVQQLTRLRHPRLLTVQHPLEESRDCLAF-CTEPVCASLANVLGN
          .F.KK.I.KY.KF..KDQI.DSLKRGV..L.R...P.L...QHPLEE..DCLAF.C.EPVCASL..VLGN
Retrocopy LFGKKVIGKYLKFL<KDQITDSLKRGV*YLIRIG*PQLYIIQHPLEEFKDCLAF<CIEPVCASLVSVLGN

Parental  WENLPSSGS-PDIKDYKLYDVETKYGLLQVSEGLSFLHSSVKMV-HGNLTPENIILNK-TGAWKIMGFDF
          WENLPS..S.PDIKDYK.YDVETKY..LQVSE.LSFLH.S.KMV...NLTPEN.ILNK..GAWKI..FDF
Retrocopy WENLPSTES<PDIKDYKFYDVETKYV*LQVSEKLSFLHNSIKMV<GENLTPENTILNK<IGAWKIIDFDF

Parental  CIPSTNPSEQEPKFPCKEWDPNLPSLCLPNPEYL-APEYILSVSCETASDMYSLGAVVYAVFNKGKPIFE
          ...S.N.S.....F..KE....L.SL.L...EYL.APE.ILS..C...S....L..VVY.VFNKGKP.FE
Retrocopy WSTSLNSSXXXSNFSSKE*VQYLLSLYLQYTEYL<APEHILSMNCVKYS----LEVVVYSVFNKGKPVFE

Parental  VNKQDIYKSF
          .NKQDI.K.F
Retrocopy INKQDIHKNF

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_569 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006752	1 retrocopy	retro_cfam_800,
Homo sapiens	ENSG00000136021	1 retrocopy	retro_hsap_2369,
Gorilla gorilla	ENSGGOG00000002948	1 retrocopy	retro_ggor_1799,
Macaca mulatta	ENSMMUG00000023600	1 retrocopy	retro_mmul_957,
Pongo abelii	ENSPPYG00000004865	1 retrocopy	retro_pabe_2139,
Sarcophilus harrisii	ENSSHAG00000011140	1 retrocopy	retro_shar_569 ,