RetrogeneDB ID: retro_shar_386

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841562.1:1611014..1611949(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERGIC2
• Ensembl ID: ENSSHAG00000004822
• Aliases: None
• Description: ERGIC and golgi 2 [Source:HGNC Symbol;Acc:30208]

Sequence

>retro_shar_386
AATATATTCAGTATATCTTAGATGAAGTATGAATATGAAGTAGACAAGGATTTCTCTAGTAAATTAAAAATTTATAAAAT
TACTGTGGCTGTGAAGTATTAGTATTTTGGAGCTGATGTATCAGATTTAGTAGAAATTATGGTTGCAGCTTCAGATAGTC
TTGTTTATGAAATCAGTAATATTTGATCTCTTACCCCAACAATGAGAGAGGTAAGAGAATGCTACAGATAATTCAAAGTA
GACTATTAGAGGAACAGTCAGTATAAGATGTGATATTCAAAAATGCTTTTAAAAGTGTTTCCACAGTATTACTTCCAAGA
GGAAATAATTCATTACAACCACCAGATGCATGCAGAATTCATGATTATCTACATTTCAGTAAAGTATTAGGGAATTTTCA
TGTAACTGTAGGCAAGGCAATTCCACATTCCCTAGATCATGCACACCTGGCAGCACTTGTCAGCCATAACTCCTACAATT
TTCCCATAGAATAGATCATTTGTTTTTTGGTGAACTTGTTCCAGGAATTATTAATCTGTTAGGTGGAACTGAAAAATTGC
TGTAGACCATAACCAGATGTTCTGGTACTTTATCACAGTTGTGCCAACAAAATTCAATACATACAAAGCAGACATTCACC
ATTTTAAAGTGACAGAAAGGGAATTGCCATTAGCCATGCAGCAGGAAGCCTTGGGGTATTTGGGATATTTATAAAATATG
ATCTTAGTTCCCTTATGATAATAGTAACTGAAGAACATATGCTGTTCTGGCAATTTTTAGTGAGACTATGTGGTATTATT
GGAGGAATTTTCTCAACAACAGGCATGCTACATGGATTTGGAAAATTCATAGTTGAAATAATTTGTTGTCATTTCAGACT
TGGAGCCTATAAACCTGTTACTTCTGTTCAGGATGGCCACACAAACAACCTCTTA

Alignment

ORF - retro_shar_386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SVYQDTWMKYEYEVDKDFSSKLRINIDITVAMKCHYVGADVLDLAETMVAPADGLVYE-PVIFDLSPQQR
          .......MKYEYEVDKDFSSKL.I...ITVA.K..Y.GADV.DL.E.MVA..D.LVYE..VIFDL.PQQ.
Retrocopy NIFSIS*MKYEYEVDKDFSSKLKI-YKITVAVKY*YFGADVSDLVEIMVAASDSLVYE>SVIFDLLPQQ*

Parental  E-WQRMLQTIQSRLQEEHSLQDVIFKSAFKSASTALPPREDNSLQPPDACRIHGHLYVNKVAGNFHITVG
          E...RMLQ.IQSRL.EE.S..DVIFK.AFKS.ST.L.PR..NSLQPPDACRIH..L...KV.GNFH.TVG
Retrocopy E>GKRMLQIIQSRLLEEQSV*DVIFKNAFKSVSTVLLPRGNNSLQPPDACRIHDYLHFSKVLGNFHVTVG

Parental  KAIPHPRGHAHLAALVSHDSYNF-SHRIDHLSFGELVPGIINPLDGTEK-IAIDHNQMFQYFITVVPTKL
          KAIPH...HAHLAALVSH.SYNF.SHRIDHL.FGELVPGIIN.L.GTEK.IA.DHNQMF.YFITVVPTK.
Retrocopy KAIPHSLDHAHLAALVSHNSYNF<SHRIDHLFFGELVPGIINLLGGTEK<IAVDHNQMFWYFITVVPTKF

Parental  NTYKISADTHQFSVTERER-AINHAAGSHGVSGIFMKYDLSSLMVTVTEEHMPFWQFLVRLCGIIGGIFS
          NTYK..AD.H.F.VTERE..AI.HAAGS.GV.GIF.KYDLSSLM..VTEEHM.FWQFLVRLCGIIGGIFS
Retrocopy NTYK--ADIHHFKVTEREL<AISHAAGSLGVFGIFIKYDLSSLMIIVTEEHMLFWQFLVRLCGIIGGIFS

Parental  TTGMLHGIGKFIVEIICCRFRLGAYKPVTSVQDGHTNNHL
          TTGMLHG.GKFIVEIICC.FRLGAYKPVTSVQDGHTNN.L
Retrocopy TTGMLHGFGKFIVEIICCHFRLGAYKPVTSVQDGHTNNLL

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_386 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015668	1 retrocopy	retro_cpor_824,
Ornithorhynchus anatinus	ENSOANG00000010582	1 retrocopy	retro_oana_32,
Oryctolagus cuniculus	ENSOCUG00000017255	1 retrocopy	retro_ocun_1540,
Pongo abelii	ENSPPYG00000004390	1 retrocopy	retro_pabe_657,
Rattus norvegicus	ENSRNOG00000001852	1 retrocopy	retro_rnor_1557,
Sarcophilus harrisii	ENSSHAG00000004822	1 retrocopy	retro_shar_386 ,
Tupaia belangeri	ENSTBEG00000011223	1 retrocopy	retro_tbel_3783,