RetrogeneDB ID: retro_shar_34

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834543.1:1033813..1034812(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000012454
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000013955
• Aliases: None
• Description: None

Sequence

>retro_shar_34
ATGGCTACAGAAAAGCAACCCGAGACCGAAGCCCCGAGAACACAGCAAACACCTTCATCCACCAATCAAAGCAAGCTTGC
ACCTCCCAATCCAAACTACACATTAAAATTTACATTAGTGGGGCATACAAAAGCTGTATCTTCGGTAAAATTTAGCCCCA
ATGGAGAATGGTTAGCGAGTTCTTCTGCTGATAAGCTCATTAAAATTTGGGGAGCATATGATGGAAAATGTGAGAAAACT
ATATCTGGGCACAAACTAGAAATCTCTGATGTTGCCTGGTCTTCAGATTCCAACCTTCTTGTGTCTGCCTCAGATGATAA
AACTCTTAAAATCTGGGATGTGAGCTCGGGAAAATGTCTAAAAACCCTGAAGGGACACAGTAATTACGTCTTTTGCTGTA
GCTTCAATCCCCTATCCAACCTCGTCGTTTCCGGCTCTTTTGATGAAAGCATAAGGATATGGGATGTGAAAACAGGAAAG
TGCCTCAAGACTTTGCCGGCTCACTCCGACCCAGTAACAGCTGTGCATTTTAATAGTGACGGATCTTTGATTGTGTCGAG
TAGTTATGATGGTCTCTGCCGAATCTGGGATACTGCGTCAGGTCAATGTTTAAAAACTCTTATTGGTGATGATAATCCTC
TTGTGTCTTTTGTAAAATTCTCTCCGAATGGTAAATACATTCTTACGGCAACTCTGGATAACCTTCTTAAGCTATGGGAC
TACAGCAAGGGGAGGTGCCTAAAGACATACACTGGTCACAAGAATGAGAAATACTGTATTTTTGCAAACTTTTTAGTCAC
TGGTGGAAAATGGATTGTGTCCGGATCAGAAGATAATCTTGTTTACATTTGGAACCTTCAGACAAAAGAGATTGTGCAGA
AATTACAAGGTCATACAGATGTTGTAATCTCCACAGCTTGTCACCCCACAGAAAACATAATTGCATCAGCTGCATTAGAA
AATGATAAAACGATTAAACTCTGGAGGAGTGACTATTAA

Alignment

ORF - retro_shar_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATEEKKPEAEATKTQSAPSSSTNQSKPAPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIK
          MATE.K.PE.EA..TQ..PSS.TNQSK.AP..PNY.LKFTL.GHTKAVSSVKFSPNGEWLASSSADKLIK
Retrocopy MATE-KQPETEAPRTQQTPSS-TNQSKLAPPNPNYTLKFTLVGHTKAVSSVKFSPNGEWLASSSADKLIK

Parental  IWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQ
          IWGAYDGK.EKTISGHKL.ISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCC.FNP.
Retrocopy IWGAYDGKCEKTISGHKLEISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCSFNPL

Parental  SNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLI
          SNL.VSGSFDES.RIWDVKTGKCLKTLPAHSDPV.AVHFN.DGSLIVSSSYDGLCRIWDTASGQCLKTLI
Retrocopy SNLVVSGSFDESIRIWDVKTGKCLKTLPAHSDPVTAVHFNSDGSLIVSSSYDGLCRIWDTASGQCLKTLI

Parental  DDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSED
          .DDNP.VSFVKFSPNGKYIL.ATLDN.LKLWDYSKG.CLKTYTGHKNEKYCIFANF.VTGGKWIVSGSED
Retrocopy GDDNPLVSFVKFSPNGKYILTATLDNLLKLWDYSKGRCLKTYTGHKNEKYCIFANFLVTGGKWIVSGSED

Parental  NLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSD
          NLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLW.SD
Retrocopy NLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWRSD

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_34 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000013955	3 retrocopies	retro_shar_34 , retro_shar_45, retro_shar_652,
Drosophila melanogaster	FBgn0040066	1 retrocopy	retro_dmel_69,