RetrogeneDB ID: retro_shar_48

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864774.1:1676512..1677385(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000015070
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000008267
• Aliases: None
• Description: None

Sequence

>retro_shar_48
ATGTTTCGACGGGAGGCTCGCCTGCGCCGGGAGTATTTGTACCGCAAAGCCCAGGAACAGAAGCAGCATCTTCTGGAGGA
GAAGAAACGAAGGCTGAAGAGGGCCCTGGAGGACAATCAGCCCATCCCACCTGAGCTCTGTCGGGAAGCTCTGACGCTCC
AGCAGGCATTGGAGTTTGATGATGTCGGAAGTGAGGATGTCCTGAACCCCCAGGATGATGAATACAGATGGGCAGGTGTA
GAAGACCCCCGGATTATGATCACTACATCTCGGGACCCCAGCTCTCGGCTCAAGATGTTTGCCAAGGAGCTGAAGCTGAT
ACTTCCCGGTGCTCAGAAAATGAACCGCGGCCGGTGTGAGATGGGCGCTCTGGTCCGTGCGTGTGAAGCCCGCGGAGTCA
CGGATCTGCTGCTGGTGCACGAGCACCGCGGAACACCGGTGGGCCTCATCGTGAGCCACCTGCCCTTTGGGCCTACCGCG
TATTTCACGCTGTGCAATGTTGTGATGCGGCACGACATCCCTGGCCTTGGCACTGCCTCAGAGGCCTTTCCCCACCTGAT
CTTCAGCGGCTTCTCCTCCCACCTGGGACAGCGGGTCTCCAGTATTCTCCGATCCCTCTTCCCGGTACCCAAGGATGATA
GCCACCGGGTCATTACCTTTGTCAACCAGGATGACTACATTTCTTTTCGGCATCATGTGTACCGGAAAACTGATCGGAGC
ACGGTGGAGCTGACGGAGGTAGGGCCGAGATTTGAGATGAAATTGTACCTGATCCGTCTGGGCACACTGGAGCACGAAGC
CTCAGCAGATGTGGAGTGGCGCTGGCACCCATATACCCACACAGCCCGAAAGAAGATCTCTCTCGGTATCTAG

Alignment

ORF - retro_shar_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRREARLRREYLYRKAQEQKQHLLEEKKLKLKQALDENQPLPTELRREALTLQKALEFDDDGSEGVLNH
          M.RREARLRREYLYRKAQEQKQHLLEEKK..LK.AL..NQP.P.EL.REALTLQ.ALEFDD.GSE.VLN.
Retrocopy MFRREARLRREYLYRKAQEQKQHLLEEKKRRLKRALEDNQPIPPELCREALTLQQALEFDDVGSEDVLNP

Parental  QDDEYRWAGVEDPRIMITTSRDPSSRLKMFAKELKLIFPGAQKMNRGRHEMGALVRACKANGVTDLLLVH
          QDDEYRWAGVEDPRIMITTSRDPSSRLKMFAKELKLI.PGAQKMNRGR.EMGALVRAC.A.GVTDLLLVH
Retrocopy QDDEYRWAGVEDPRIMITTSRDPSSRLKMFAKELKLILPGAQKMNRGRCEMGALVRACEARGVTDLLLVH

Parental  EHRGTPVGLIVSHLPFGPTAYFTLCNVVMRHDVPDLGTAPQAFPHLIFHGFSSRLGQRVSDILRYLFPVP
          EHRGTPVGLIVSHLPFGPTAYFTLCNVVMRHD.P.LGTA..AFPHLIF.GFSS.LGQRVS.ILR.LFPVP
Retrocopy EHRGTPVGLIVSHLPFGPTAYFTLCNVVMRHDIPGLGTASEAFPHLIFSGFSSHLGQRVSSILRSLFPVP

Parental  KDESRRVITFANQDDFISFRHHVYRKPDHHTVELTEVGPRFEMKLYMIRLGTLEQEATADVEWRWHPYTH
          KD.S.RVITF.NQDD.ISFRHHVYRK.D..TVELTEVGPRFEMKLY.IRLGTLE.EA.ADVEWRWHPYTH
Retrocopy KDDSHRVITFVNQDDYISFRHHVYRKTDRSTVELTEVGPRFEMKLYLIRLGTLEHEASADVEWRWHPYTH

Parental  TARKRTFLSI
          TARK...L.I
Retrocopy TARKKISLGI

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_48 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016200	2 retrocopies	retro_etel_1844, retro_etel_73,
Macropus eugenii	ENSMEUG00000008058	1 retrocopy	retro_meug_1463,
Sarcophilus harrisii	ENSSHAG00000008267	1 retrocopy	retro_shar_48 ,