RetrogeneDB ID: retro_shar_128

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834419.1:1315370..1315717(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRGBP
• Ensembl ID: ENSSHAG00000010685
• Aliases: None
• Description: MRG/MORF4L binding protein [Source:HGNC Symbol;Acc:15866]

Sequence

>retro_shar_128
CATAATATGCAAGTATTTCATGAATCTAAGATTCTTCCATTTTTTAATTTAGCAAAGAACATCAACCTTCTTGATAAAAT
TATCTAAAATATCAAAAAAGGAAAAATAATTGGAGATGCGATGAAAGAAGAAATGAAGGAAGACATCGATCTACACCATC
TTTTTACATTTTCAGGAAACTTGGGGACAGCAGGTCAAAAATACATTGGCAAAGAGAAGGAGAAGAGCAAACAGGTTCTA
GATCTAATGAAGGTGCAGCTAAAAGGAAATATAATTGGGTCACAGAAAATGTCTTAAAATGCAAACATCAATCCTCCAGC
CCAAGTGCAGCCAAGTTTTGAAGAACA

Alignment

ORF - retro_shar_128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.1 %
• Parental protein coverage: 62.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YDMQALHESEILPFPNSEKNFILPEEIIQEVKEGKVMIEDEMKEEIKEEVDPHTGTEDVFTSSGNLGKGA
          ..MQ..HES.ILPF.N..KN..L...II...K.GK..I.D.MKEE.KE..D.H......FT.SGNLG...
Retrocopy HNMQVFHESKILPFFNLAKNINLLDKII*NIKKGKI-IGDAMKEEMKEDIDLH----HLFTFSGNLGTAG

Parental  EKSSGKEKEKSS-SDSGSKEGADKRKRNRVTEKVLNANSNPSSPSAAKRRRT
          .K..GKEKEKS....S.S.EGA.KRK.N.VTE.VL......SSPSAAK..RT
Retrocopy QKYIGKEKEKSK<TGSRSNEGAAKRKYNWVTENVLKCKHQSSSPSAAKF*RT

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_128 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000020272	1 retrocopy	retro_cpor_1438,
Monodelphis domestica	ENSMODG00000016803	1 retrocopy	retro_mdom_246,
Mus musculus	ENSMUSG00000027569	1 retrocopy	retro_mmus_1383,
Sarcophilus harrisii	ENSSHAG00000010685	1 retrocopy	retro_shar_128 ,
Ictidomys tridecemlineatus	ENSSTOG00000012953	1 retrocopy	retro_itri_634,