RetrogeneDB ID: retro_shar_342

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841397.1:2467890..2468845(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSRP1
• Ensembl ID: ENSSHAG00000003513
• Aliases: None
• Description: nuclear speckle splicing regulatory protein 1 [Source:HGNC Symbol;Acc:25305]

Sequence

>retro_shar_342
GAGGCAGAAAGAGAGAGGAGAGCCGCTGCCCTGGAGGCTCGACTGGATGTAACCAAGCAGAAGGATCTCAGTGGATTTTT
ATAGACACTTTTTAAATCAAACAGTTGGAGAAGAGGAAGTCCCTAAATGCAAGCCTTTGGGAAGCCAGCTCTGGGATAAA
GGAGGAGAAGCCGCGGGGTTATTTGGAGGAACGGAATCCAGAGGCGGAGTCCGGGAGGATAGAGCCAGGCCCGAAACCAG
AGTGAAGGAAGAGGAAAATCCGGACGCGGACAGCGACCTGGAGGAGGAGGGCAGTGAGGAGGAGGAGAACGGGGCCGGCC
GGGGCCGCCGGCATTCTAGGTCCTCGGGGGAGGACCGGGGGCCGGCCACAGGAGCTGCAGGGCCGGGGGCAGCGACCCAG
CTGGGGGGGACCGCGCAGTCCGGCGTCGGGACCAACGTTCCCATGACGGCGCTAGCCAGAAAGAACAAGCCGAGAAGTAC
AAGCTCAGGGAGGACAGCGGTAAAGACCACGTCCGGAAGAGGCAGGGGAGAGGGGGAAGAGAGAAGGACTGAGGCAGAGG
CGGGAACATGGTGGGGAGAAGCAGGCTCCCCGGGACCGAGAGCCAGAGCCAGCCCGGAGGAGAAACAGTGGAGACCCTTA
GGACGATCCGGAGCGGGAGGAGGCCGAGGCTGCCCAGAGGCCCGGGCAGACTGCCCGGAGAGAAGCAGGGACAAGGAGCC
GGGCCTCGGGCCTTCGCAGAGCGAGGGGAGCGCGGGGCCTGGGGCTCGAGACGGGTTGCCTCGGGGGGACGCAGAGGGGG
CCTCCAAACGCCAGCACGAGGAGGGGGCAGAGAAGCCCCGTGAGGTGCTGAGCAAGTTTGCAAAGCGCAGCCGCCAAGAG
ATGGTGATGTCGGCCCGAGACCGCTACCTGGCCCGACAGGTGCTGCTGCGCGGCCAAAAGCTACATTGAGAAAGA

Alignment

ORF - retro_shar_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 75.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EAERERRAAALEARLDVTKQKDLSGF-YRHLLNQTVGEEEVPKC-SLREASSRIKEEKPRGYSDECNPD-
          EAERERRAAALEARLDVTKQKDLSGF.YRH.LNQTVGEEEVPKC.SL.EASS.IKEEKPRGY..E.NP..
Retrocopy EAERERRAAALEARLDVTKQKDLSGF>YRHFLNQTVGEEEVPKC>SLWEASSGIKEEKPRGYLEERNPE<

Parental  GGVRDDRARPETKVKEEENPDADSDLEES-SEEEGNKASRGCRHSSSSGEDRGPS-NRSCRTGGSDPAGG
          GGVR.DRARPET.VKEEENPDADSDLEE..SEEE.N.A.RG.RHS.SSGEDRGP...RSCR.GGSDPAGG
Retrocopy GGVREDRARPETRVKEEENPDADSDLEEEGSEEEENGAGRGRRHSRSSGEDRGPA<HRSCRAGGSDPAGG

Parental  DRAVRRRDQRSPDSARQKEKAKKYKPREDSGKDHVRKRREPDERGGGKGEERRTEREDGGEKRASRDQER
          DRAVRRRDQRS.D.A.QKE.A.KYK.REDSGKDHVRKR.....RGG......R.....G...........
Retrocopy DRAVRRRDQRSHDGASQKEQAEKYKLREDSGKDHVRKRQ---GRGGREKD*GRGGNMVGRSRLPGTESQS

Parental  EPA-RRRNNGDPQDSPERV-GGRGCAEGRADRPERSRDKEPGLGPSESEGSAGPGVQDGLPRGDAEGASK
          .P..RR.N.GDP.D.PER..GGRGC.E.RAD.PERSRDKEPGLGPS.SEGSAGPG..DGLPRGDAEGASK
Retrocopy QPG<RR-NSGDP*DDPERE<GGRGCPEARADCPERSRDKEPGLGPSQSEGSAGPGARDGLPRGDAEGASK

Parental  RQQEEGAEKPREALSKFAKRSSQETVMSARDRYLARQVARCAAKSYIEK
          RQ.EEGAEKPRE.LSKFAKRS.QE.VMSARDRYLARQV.....K...E.
Retrocopy RQHEEGAEKPREVLSKFAKRSRQEMVMSARDRYLARQVLLRGQKLH*ER

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_342 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009868	1 retrocopy	retro_mdom_391,
Pongo abelii	ENSPPYG00000008130	1 retrocopy	retro_pabe_457,
Pan troglodytes	ENSPTRG00000008957	1 retrocopy	retro_ptro_162,
Sarcophilus harrisii	ENSSHAG00000003513	1 retrocopy	retro_shar_342 ,