RetrogeneDB ID: retro_shar_72

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856865.1:112331..113039(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000004597
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000015970
• Aliases: None
• Description: None

Sequence

>retro_shar_72
ATGTCATGCTATGGGAGGTACGGAGGAGAGACCAAAGTATATGTTGGCAACCTAGAAACTGGTGCTGGCAAAGGAGAATT
AGAAAGAGCTTTTAGTTATTATGGTCCCTTAAGAACCGTATGGATTGCCAGAAATCCTCCAGGATTTGCCTTTGTGGAGT
TTGAAGATCCAAGAGATGCAGAAGATGCAGTTCAAGGACTAGATGGAAAGGTGATTTGTGGTTCTCGTGTAAGAGTCGAA
TTGTCAACAGGCCTTCCTCGAAGATCTCGGTATGATAGACCACCTGCACGCTGCCCATTTGATCCTAATGACAGATGTTA
TGAGTGTGGTGAGAAAGGTCATTATGCTTATGATTGTCACCGGTACAGCCGTCGAAGGAGAAGTAGATCACGCTCTAGAT
CTCACTCAAGATCCCGAGGAAGGAGATATTCTCGCTCACGAAGCAGGAGCCGTGGAAGGAGGTCAAGATCTGCATCTCCT
CGAAGACCAAGATCTGCATCTCTGCGTAGATCTCGATCTCCTTCAATCCAATCTCGATCTGGTTCTTTGAAAAGATCAAG
ATCATCCCGTTCAAGATCCAGATCCAGATCCAGATCTCTTTCAAGACCTAGGAGCAGCCGATCAAAGTCCAGATCACCAT
CTCCAAAGAGAAGCCACTCTCCTTCTGGAAGTCCTCGCAGGAGTGCAAGTCCTGAAAGAATGGACTAA

Alignment

ORF - retro_shar_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.7 %
• Parental protein coverage: 98.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSRSFFKTKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVIC
          Y.R....TKVYVGNL.TGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAV.GLDGKVIC
Retrocopy YGRYGGETKVYVGNLETGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVQGLDGKVIC

Parental  GSRVRVELSTGMPRRSRYDRPPARRPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRGRRY
          GSRVRVELSTG.PRRSRYDRPPAR.PFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRGRRY
Retrocopy GSRVRVELSTGLPRRSRYDRPPARCPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRGRRY

Parental  SRSRSRSRGRRSRSASPRRSRSASLRRSRSASIRSRSGSLKRSRYFQSSRSRSRSRSLSRPRSSRSKSRS
          SRSRSRSRGRRSRSASPRR.RSASLRRSRS.SI.SRSGSLKRSR....SRSRSRSRSLSRPRSSRSKSRS
Retrocopy SRSRSRSRGRRSRSASPRRPRSASLRRSRSPSIQSRSGSLKRSR-SSRSRSRSRSRSLSRPRSSRSKSRS

Parental  PSPKRSRSPSGSPRRSASPERMD
          PSPKRS.SPSGSPRRSASPERMD
Retrocopy PSPKRSHSPSGSPRRSASPERMD

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_72 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015988	1 retrocopy	retro_amel_1025,
Canis familiaris	ENSCAFG00000029620	1 retrocopy	retro_cfam_652,
Dasypus novemcinctus	ENSDNOG00000007821	2 retrocopies	retro_dnov_317, retro_dnov_829,
Macropus eugenii	ENSMEUG00000016459	1 retrocopy	retro_meug_1048,
Myotis lucifugus	ENSMLUG00000009536	2 retrocopies	retro_mluc_2005, retro_mluc_972,
Monodelphis domestica	ENSMODG00000008669	1 retrocopy	retro_mdom_289,
Mus musculus	ENSMUSG00000024097	1 retrocopy	retro_mmus_3288,
Otolemur garnettii	ENSOGAG00000010169	2 retrocopies	retro_ogar_3467, retro_ogar_3481,
Rattus norvegicus	ENSRNOG00000027360	11 retrocopies	retro_rnor_1535, retro_rnor_1977, retro_rnor_1984, retro_rnor_2419, retro_rnor_2420, retro_rnor_2421, retro_rnor_2495, retro_rnor_2501, retro_rnor_2502, retro_rnor_2503, retro_rnor_478,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sarcophilus harrisii	ENSSHAG00000015970	1 retrocopy	retro_shar_72 ,