RetrogeneDB ID: retro_shar_4

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867598.1:1159456..1160509(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000013075
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000010757
• Aliases: None
• Description: None

Sequence

>retro_shar_4
CGCGCGCTCCCACCAGGCCCTCTGTCCTTGTCTGCCTCTGGGAGGACCAATTTTGCCAGTACCATGGCAGCAGCCTTTTG
GGGGTACCAGGGACCCTCGGACTATTTGTATGAGATGCAGAAGCAGTTTCGCAACTGTGGGAAGACTGAAGAATACAAGG
CCCACTCGGCTAACATATTCTCGGTAGCCTGGAGCTGTGATGGGGCTCGCCTGGCTTCGGGCTCTCTCGATAACACCGCC
AGCGTCTTCCTCCTGAAAGAAAACTGCCTGGTAAGAGAGTACAACTACCAAGGCCACACCAACCGAGTGAACCAGCTGTG
TTGGCACCCCAGCAACCCCGATCTCTTTGTAACTGCCTCGGAGGATCGGAGCGTTCGCATCTGGGATGTGCGCAAAATGA
AGTGCGTCATCGTCATCAGCACCAAAGGCGAGAATATGAATATATGCTGGAGTCCCGATGGTCGAACCATTGCCGTGGGC
AACAGGCGAGACGTGGTCACCTTCATCGACGCTCGCACCAACCGGGCCAAGGCGGAGGAGCAATTCAGCTACGAGGTCAA
CGAGATATCCTGGAACAACGACAACACCCAGTTCTTCCTTACCAATGGCAAGGGCTTCATCACTATCCTCAGTTACCCTG
ATCTAAAGCCTGTGCAGTTACTCAACGCCCATACTTCCAACTGCATCTGTATCAAGTTCGATCCCACCAGCAAGTATTTC
GCCACAGGAAGCACCGATTCCCTAGTGAGTCTCTGGGATCTTAACGAGCTGGTGTGTGTGAGGTGCCTGTCCAGGCTGGA
CTGGCCCGTGACGAGTCTCAGTTTCAGCCACGATGGGAAAATGCTGGCATCGGCATCCGAGGATCTCTTCATTGATATTG
CTGAGGTGGAGACTGGCGAAAGGATCTGGGAGATACAGTGTCAATCTTCCACTTTCAGTGTGGCCTGGCATCCCAAATTT
CCACTGTTAGCTTTTGCTTGTGATGACAAAGAAAATCTACCAGAAGCTTGCCGAGAGACTGGAACCGTGAAGCTGTTTGG
GCTTCCTAACTAA

Alignment

ORF - retro_shar_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.84 %
• Parental protein coverage: 90.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLAPRPSRGALGMQELFRSHSKTREFAAHSATGDSVAWSCDGRRLASGSFDKTASVFLLEKDRLVKENNY
          W....PS.....MQ..FR...KT.E..AHSA...SVAWSCDG.RLASGS.D.TASVFLL....LV.E.NY
Retrocopy WGYQGPSDYLYEMQKQFRNCGKTEEYKAHSANIFSVAWSCDGARLASGSLDNTASVFLLKENCLVREYNY

Parental  RGHGDSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKCIATVNTKGENINICWSPDGQTIAVGNKDDVV
          .GH...V.QLCWHPSNPDLFVTAS.D...RIWDVR..KC.....TKGEN.NICWSPDG.TIAVGN..DVV
Retrocopy QGHTNRVNQLCWHPSNPDLFVTASEDRSVRIWDVRKMKCVIVISTKGENMNICWSPDGRTIAVGNRRDVV

Parental  TFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINILSYPELKPVQSINAHPSNCICIKFDPT
          TFIDA.T.R.KAEEQF..EVNEISWNNDN..FFLTNG.G.I.ILSYP.LKPVQ..NAH.SNCICIKFDPT
Retrocopy TFIDARTNRAKAEEQFSYEVNEISWNNDNTQFFLTNGKGFITILSYPDLKPVQLLNAHTSNCICIKFDPT

Parental  GKYFATGSADALVSLWDVDELVCVRCFSRLDWPVRTLSFSHDGKMLASASEDHFIDIAEVETGDKLWEVQ
          .KYFATGS.D.LVSLWD..ELVCVRC.SRLDWPV..LSFSHDGKMLASASED.FIDIAEVETG...WE.Q
Retrocopy SKYFATGSTDSLVSLWDLNELVCVRCLSRLDWPVTSLSFSHDGKMLASASEDLFIDIAEVETGERIWEIQ

Parental  CESPTFTVAWHPKRPLLAFACDDKDGKYDSSREAGTVKLFGLPN
          C.S.TF.VAWHPK.PLLAFACDDK.......RE.GTVKLFGLPN
Retrocopy CQSSTFSVAWHPKFPLLAFACDDKENLPEACRETGTVKLFGLPN

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_4 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006495	2 retrocopies	retro_cjac_1571, retro_cjac_3072,
Macropus eugenii	ENSMEUG00000001068	2 retrocopies	retro_meug_1061, retro_meug_19,
Monodelphis domestica	ENSMODG00000005339	1 retrocopy	retro_mdom_164,
Mus musculus	ENSMUSG00000025872	2 retrocopies	retro_mmus_1821, retro_mmus_441,
Otolemur garnettii	ENSOGAG00000003503	1 retrocopy	retro_ogar_3005,
Sarcophilus harrisii	ENSSHAG00000010757	1 retrocopy	retro_shar_4 ,