RetrogeneDB ID: retro_shar_574

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850266.1:15162..15837(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APIP
• Ensembl ID: ENSSHAG00000011523
• Aliases: None
• Description: APAF1 interacting protein [Source:HGNC Symbol;Acc:17581]

Sequence

>retro_shar_574
CAGGACAAGGAACATCCAAGAAATTTGATTTCAGAGCTCAGCAAACAGTTTTATCATTTGGGCTGGGTCACTGGGACTGG
CAGAGGAATTAGCTTGAAGCATGGCAATGAAATCTACATTGCTCCATCAGGAGTGCAAAAAGAATGAATTCAGCCTGAAG
ACATGTTTTTTTTTGACATAAATGAACAGGACATCAGTGGACCTCCACCATACAAGAATCTAAGAAAAAGTCAGTGTACA
CCTCTCTTTATGAATGCTTACACTATGAGAGGATTAGGAGCAGTGATCCATACTCATTCTAAGGCTGCTGTGATGGCCAC
CTTTCTCTTTCCAGGATGAGAGTTTAAAATTACACATCAGGAGATGATAAAAGGAATCAGGAAATACACCTCTGGAGGTT
GTTACAGATATGATGATATGTTAGTGGTCCCCATTATTGAGAATACACCAGAGGAAAAGGACCTCAAAGAATGAATGACT
CAAGCAATGAATGAATACCCCGATTCCTGTGCTGTTTTAGTCAGGCACCATGGGGTATACATGTTTGGGGAGAAACATGG
GAAAAAGCTAAAACCATGTTGTGAGTGTTACGACTACTTGTTCGATATTGCAGTGTCAATGAAGAAATTAGGGCTGGAGC
CTAGCCAGCATCCAGTTGGAGAAAATGGAATTCTC

Alignment

ORF - retro_shar_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.0 %
• Parental protein coverage: 94.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDKEHPRNLIPELCKQFYHLGWVTGTGGGISLKHGNEIYIAPSGVQKERIQPDDMFVCDINEQDISGPPP
          .DKEHPRNLI.EL.KQFYHLGWVTGTG.GISLKHGNEIYIAPSGVQKE.IQP.DM...DINEQDISGPPP
Retrocopy QDKEHPRNLISELSKQFYHLGWVTGTGRGISLKHGNEIYIAPSGVQKE*IQPEDMXXXDINEQDISGPPP

Parental  YKNLRKSQCTPLFMNAYTMRGAGAVIHTHSKAAVMATLLFPGREFKITHQEMIKGIRKCTSGGCYRYDDM
          YKNLRKSQCTPLFMNAYTMRG.GAVIHTHSKAAVMAT.LFPG.EFKITHQEMIKGIRK.TSGGCYRYDDM
Retrocopy YKNLRKSQCTPLFMNAYTMRGLGAVIHTHSKAAVMATFLFPG*EFKITHQEMIKGIRKYTSGGCYRYDDM

Parental  LVVPIIENTPEEKDLKERMAQAMNEYPDSCAVLVRRHGVYVWGET-WEKAKTMCECYDYLFDIAVSMKKL
          LVVPIIENTPEEKD...........YPDSCAVLVR.HGVY..GE....K.K..CECYDYLFDIAVSMKKL
Retrocopy LVVPIIENTPEEKDXXXXXXXXXXXYPDSCAVLVRHHGVYMFGEKHGKKLKPCCECYDYLFDIAVSMKKL

Parental  GLDPSQPPVGENGIL
          GL.PSQ.PVGENGIL
Retrocopy GLEPSQHPVGENGIL

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_574 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016758	1 retrocopy	retro_etel_220,
Homo sapiens	ENSG00000149089	1 retrocopy	retro_hsap_4208,
Gorilla gorilla	ENSGGOG00000022940	2 retrocopies	retro_ggor_2818, retro_ggor_2873,
Ornithorhynchus anatinus	ENSOANG00000007394	6 retrocopies	retro_oana_108, retro_oana_109, retro_oana_121, retro_oana_63, retro_oana_85, retro_oana_96,
Pongo abelii	ENSPPYG00000003361	1 retrocopy	retro_pabe_3442,
Pan troglodytes	ENSPTRG00000003499	1 retrocopy	retro_ptro_2856,
Sarcophilus harrisii	ENSSHAG00000011523	1 retrocopy	retro_shar_574 ,
Ictidomys tridecemlineatus	ENSSTOG00000004390	1 retrocopy	retro_itri_1029,