RetrogeneDB ID: retro_shar_822

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867585.1:551082..551514(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLGRKT
• Ensembl ID: ENSSHAG00000001757
• Aliases: None
• Description: plasminogen receptor, C-terminal lysine transmembrane protein [Source:HGNC Symbol;Acc:23633]

Sequence

>retro_shar_822
CTTTTTTCAAAGCATATGAATGAAAGTACTAAGCAGCAGCAGGAATGGATGCTCATAAATGTTTGACTTTAGATGAAAGG
CAATTAGCAATAGACAATGAAGGGAGAGAGAGGCAGATGGCTGTACAGATTGCTTGGACAAGAGAACTCCTCAAATATTT
GGGGAAAATTTTTGTCATTGCTGCCATGAGTCTCACAGCTGGAGCGATCGCAAAAGAAGCAACTGTACCTCTTTCTCCCT
GTTGTTACATTAAGCTTTATCCTTGCTTATCAATATGCTATTGATTATGGAACTCTTGTGCTGAAGAAGAAAGACAAAGC
AGAAAACATACTGAATGCAGAGAGTAGCAAGGCGTAGATTCCAAGAGGGGTGACTAATTTTGAAAACATTGAATAGTCCA
GAAAAACTCCGAGGAAATTCTTCATAGAACAA

Alignment

ORF - retro_shar_822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.85 %
• Parental protein coverage: 97.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IISKPMNENMKQQQEFMLMNARLQM-ERQLMIQNEMRERQMAMQIAWTREFLKYFGTFFGLAVIGLTAGA
          ..SK.MNE..KQQQE.ML.N..L.M.ERQL.I.NE.RERQMA.QIAWTRE.LKY.G..F..A...LTAGA
Retrocopy LFSKHMNESTKQQQEWMLINV*L*M<ERQLAIDNEGRERQMAVQIAWTRELLKYLGKIFVIAAMSLTAGA

Parental  I-KKRQPVFFVPVIPLSFVFAYQYDMGYGTLLQRMKGEAEHILDIENNKLQLPKGMITFETIEKARKAQS
          I..K.Q...F.PV..LSF..AYQY...YGTL....K..AE.IL..E..K...P.G...FE.IE..RK...
Retrocopy I>QKKQLYLFLPVVTLSFILAYQYAIDYGTLVLKKKDKAENILNAESSKA*IPRGVTNFENIE*SRKTPR

Parental  KFFIEK
          KFFIE.
Retrocopy KFFIEQ

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_822 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004320	1 retrocopy	retro_dnov_1300,
Dipodomys ordii	ENSDORG00000000109	1 retrocopy	retro_dord_553,
Otolemur garnettii	ENSOGAG00000003280	1 retrocopy	retro_ogar_2243,
Sarcophilus harrisii	ENSSHAG00000001757	1 retrocopy	retro_shar_822 ,