RetrogeneDB ID: retro_shar_394

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841587.1:1828930..1829503(+)
• Located in intron of: ENSSHAG00000015391

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC94
• Ensembl ID: ENSSHAG00000010428
• Aliases: None
• Description: coiled-coil domain containing 94 [Source:HGNC Symbol;Acc:25518]

Sequence

>retro_shar_394
ATGGCCCTTCTCTAAATGAAAGATAAGACATGTGGCAAATATATTTATAAAGATAAGAAATTTAGTGCCCAGAAGGAGAC
AGTGCAGACTGAGATATATCTGGGATTTCCAGTTTTTCATTTCTATATGAAATGTACCTGTTGTCTAGCTCAAAATAACC
TTCAAAATAAACTCTGAGAAAACAGATTATATCATGGAACATGGAGCTATCTGAAACATCCAGGAACTCTGGAAAGAAGA
AGAGAAAAGGACACAGAAGGAAAGAGAAAGTGAAGAATCCCATAATCCCAGAAGATGCTGGAGAACCAGATCAAGGACTC
CAAGCTGGAGGTGGATGTTCTGGAGAACTTGAAGTAGTTGAAGGAGCATGATCAGCACTAGGCTAATGTGGACTTTAAAT
GATGTTCCAGAAGCACCCATTGTCCAACTGTCTGAGAAAGAGAAGCACCAGTAAGAGCAGGAGGAGGGACCAAAAAAGAA
ATGGATGCCATGATGGAACAGGCAGAGAAGATTTTGACACTGATGAATAGCCTGCCCTTGCATTTTCCCAGTTGCCTTTG
CAGTCCAATTCCC

Alignment

ORF - retro_shar_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.81 %
• Parental protein coverage: 58.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAPFNMRCKTCGEYIYKGKKFNARKETVQNELYLGLPIFRFYIKCTRCLAE-ITFKTDPENTDYTMEHGA
          MA...M..KTCG.YIYK.KKF.A.KETVQ.E.YLG.P.F.FY.KCT.CLA..ITFK...E.TDY.MEHGA
Retrocopy MALL*MKDKTCGKYIYKDKKFSAQKETVQTEIYLGFPVFHFYMKCTCCLAQ>ITFKINSEKTDYIMEHGA

Parental  TRNFQAEKLLEEEEKRVQKEREDEELNNP-MKVLENRTKDSKLEMEVLENLQELKELNQRQANVDFE-AM
          ..N.Q...L..EEEKR.QKERE.EE..NP..K.LEN..KDSKLE..VLENL..LKE..Q..ANVDF...M
Retrocopy I*NIQ--ELWKEEEKRTQKERESEESHNP<QKMLENQIKDSKLEVDVLENLK*LKEHDQH*ANVDFK<MM

Parental  LQQHRVS---EEEKRQREQEEDQ-REMEAMMEQARRRRLIEDSDSDEEPALTPSQLP
          .Q.H..S..............DQ..EM.AMMEQA........S.....P....S..P
Retrocopy FQKHPLSNCLRKRSTSKSRRRDQ>KEMDAMMEQAEKILTLMNSLPLHFPSCLCSPIP

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_394 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022785	1 retrocopy	retro_ecab_347,
Monodelphis domestica	ENSMODG00000000841	1 retrocopy	retro_mdom_496,
Mus musculus	ENSMUSG00000003208	1 retrocopy	retro_mmus_1640,
Otolemur garnettii	ENSOGAG00000001662	1 retrocopy	retro_ogar_168,
Sarcophilus harrisii	ENSSHAG00000010428	1 retrocopy	retro_shar_394 ,