RetrogeneDB ID: retro_shar_769

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864757.1:196506..197044(-)
• Located in intron of: ENSSHAG00000005871

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000004058
• Aliases: None
• Description: None

Sequence

>retro_shar_769
CCAAGCCAAACACTCAAGATAATTCAGCCATTTGCGGAGTCAACTTCTATCAAGGCTTTATCCAAAAGGAAGCTTTGTAA
TGACCAAGTAGCATCCAAGTCTTCTAACACAGATGTTTCTTTAGATCTAGAGCATAGTGAAAATGAAAATTTAGAAGAAG
TCTCTCAAGAAGCTTTTGATCTCATAATTAAAGAAAATCCTCCTTCTCAGTACTGGAAAGAAGTGGCAGAAAAATGGAGG
AAAGCTCTTTATGAAGTACAACAAGAAAATGAGAAACTATATAAAAAAAGTGAACAGAAGAACAATGAAATTGCCCACTT
AAAAGAAGAAAATAAGGAATTGTCATAACTAGCAGGACATATGGCAGATATGATAGAAAGGCTCACTGGGTAATCTCTAG
AAAACTTTGAACCACAAAACAATCCAGTATTTGAAGATTCTGGGAGGTGAAGAAGCAGGCAGTGATTTAGAACAAAACCA
CCTTGCTACATGTGATGAAAAAAATGCTTCTTTACCTACAGATGGATGACCATGTGTA

Alignment

ORF - retro_shar_769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.14 %
• Parental protein coverage: 85.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTAAGSLVGRVKESTSIKALSKRKLWNDQVTSKSSNNDVALDPEHSENENLEEVSQEAFDLMINENPPPQ
          P...........ESTSIKALSKRKL.NDQV.SKSSN.DV.LD.EHSENENLEEVSQEAFDL.I.ENPP.Q
Retrocopy PSQTLKIIQPFAESTSIKALSKRKLCNDQVASKSSNTDVSLDLEHSENENLEEVSQEAFDLIIKENPPSQ

Parental  YWKEVAEQRRKALYEALQENEKLHKEIEQKDNEIARLKEENKELAELAEHVQYMADMIERLTGQSLENFE
          YWKEVAE..RKALYE..QENEKL.K..EQK.NEIA.LKEENKEL..LA.H...MADMIERLTG.SLENFE
Retrocopy YWKEVAEKWRKALYEVQQENEKLYKKSEQKNNEIAHLKEENKELS*LAGH---MADMIERLTG*SLENFE

Parental  PRNNPAFEDSDS-GGEEAGSDLEQNRLATCEEKNASLPTDKITCI
          P.NNP.FE..DS.GGEEAGSDLEQN.LATC.EKNASLPTD...C.
Retrocopy PQNNPVFE--DS>GGEEAGSDLEQNHLATCDEKNASLPTDG*PCV

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_769 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006161	1 retrocopy	retro_cjac_1012,
Microcebus murinus	ENSMICG00000014010	1 retrocopy	retro_mmur_594,
Myotis lucifugus	ENSMLUG00000014849	2 retrocopies	retro_mluc_1589, retro_mluc_743,
Monodelphis domestica	ENSMODG00000011682	1 retrocopy	retro_mdom_1800,
Mus musculus	ENSMUSG00000006715	2 retrocopies	retro_mmus_1525, retro_mmus_2213,
Oryctolagus cuniculus	ENSOCUG00000000728	1 retrocopy	retro_ocun_613,
Otolemur garnettii	ENSOGAG00000004982	1 retrocopy	retro_ogar_1726,
Ochotona princeps	ENSOPRG00000007969	1 retrocopy	retro_opri_439,
Rattus norvegicus	ENSRNOG00000018782	1 retrocopy	retro_rnor_820,
Sarcophilus harrisii	ENSSHAG00000004058	2 retrocopies	retro_shar_581, retro_shar_769 ,
Tupaia belangeri	ENSTBEG00000010502	2 retrocopies	retro_tbel_1028, retro_tbel_353,