RetrogeneDB ID: retro_shar_86

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL857016.1:324059..324977(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000007519
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000014762
• Aliases: None
• Description: None

Sequence

>retro_shar_86
ATGGATAAAAGACGCTGTGTTCCTCCACTAGAGCCCAAGTTGGCAGCAGGCTGTTGCGGGGTAAAGACGCCTAAATTATC
AGGAAGTGGAACACACAGTCACGGGAACCAGTCAACAACTGTACCTGGCTCTAGTTCAGGTCCTCTTCAGAGCCACCAGC
ATGTGGATGGGAGCAATGGAAGGGAGAATGTGTCTCACTTAACTCTGGGGCCTGGAAATTCCCCAATTACTCGAATGAAT
CCCACTTGGGGAGCTCTGAGCCCACTTTCCCAGCCCAGTGGAACTGCCAATACCACCAAGAATCTGGTGGTGACAGCGGA
AATGTGCTGCTACTGCTTCGATGTCCTCTATTGCCATCTCTATGGCTTCTCCCAGCCACGACTTCCTAGATTCACCAATG
ACCCCTACCCACTCTTTGTGACATGGAAGATGGGGAGAGACAAACAGCTTCGTGGCTGCATTGGAACCTTCTCGGCCATG
AATCTTCATTCAGGACTCAGGGAATACGCATTAACCAGTGCACTTATGGACAGCAGATTTCCCCCCCTGACCCGCGAGGA
GCTGCCTAAACTTTTCTGCTCTGTCTCCCTTCTTACTAACTTTGAGGATGCCAGTGACTACCTTGACTGGGAGGTAGGGG
TACATGGGATTCGAATTGAGTTCATCGACGAAAAAGGTGTTAAAAGGACAGCCACATATTTACCTGAGGTCGCTAAGGAA
CAAGATTGGGATCAGATCCAGACAATAGACTCCTTGCTCAGGAAAGGCGGCTTTAAGGCTCCAATTACCAATGAATTTAG
AAAAACAATTAAACTCACCAGATACCGCAGCGAGAAAGTGACAATCAGTTATGCAGAGTATATTGCTTCTCGTCATGGCA
CTCTTCATGCCCCACCGCTCTACAATCATTACTCCTGA

Alignment

ORF - retro_shar_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.53 %
• Parental protein coverage: 93.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRRCVPPLEPKLAAGCCGVKKPKLSGSGTHSHGNQSTTVPGSSSGPLQNHQHVDGSNGRENVSDLTLG
          M.KRRCVPPLEPKLAAGCCGVK.PKLSGSGTHSHGNQSTTVPGSSSGPLQ.HQHVDGSNGRENVS.LTLG
Retrocopy MDKRRCVPPLEPKLAAGCCGVKTPKLSGSGTHSHGNQSTTVPGSSSGPLQSHQHVDGSNGRENVSHLTLG

Parental  PGNSPITRMNPTSGALSPLSRPNGTANTTKNLVVTAEMCCYCFDVLYCHLYGFPQPRLPRFTNDPYPLFV
          PGNSPITRMNPT.GALSPLS.P.GTANTTKNLVVTAEMCCYCFDVLYCHLYGF.QPRLPRFTNDPYPLFV
Retrocopy PGNSPITRMNPTWGALSPLSQPSGTANTTKNLVVTAEMCCYCFDVLYCHLYGFSQPRLPRFTNDPYPLFV

Parental  TWKTGRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFPPLTREELPKLFCSVSLLTNFEDASDYLDW
          TWK.GRDK.LRGCIGTFSAMNLHSGLREY.LTSAL.DSRFPPLTREELPKLFCSVSLLTNFEDASDYLDW
Retrocopy TWKMGRDKQLRGCIGTFSAMNLHSGLREYALTSALMDSRFPPLTREELPKLFCSVSLLTNFEDASDYLDW

Parental  EVGVHGIRIEFINEKGVKRTATYLPEVAKEQDWDQIQTIDSLLRKGGFKAPITNEFRKTIKLTRYRSEKV
          EVGVHGIRIEFI.EKGVKRTATYLPEVAKEQDWDQIQTIDSLLRKGGFKAPITNEFRKTIKLTRYRSEKV
Retrocopy EVGVHGIRIEFIDEKGVKRTATYLPEVAKEQDWDQIQTIDSLLRKGGFKAPITNEFRKTIKLTRYRSEKV

Parental  TISYAEYIASR
          TISYAEYIASR
Retrocopy TISYAEYIASR

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_86 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86 ,