RetrogeneDB ID: retro_shar_114

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856958.1:315666..316962(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000007430
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EHD3
• Ensembl ID: ENSSHAG00000013011
• Aliases: None
• Description: EH-domain containing 3 [Source:HGNC Symbol;Acc:3244]

Sequence

>retro_shar_114
ATGTTCAAGTCGACCAAGGAATCAGACCGTAGGAAGTCTTATCTCTTCATGTCTGTGGCCCAGAGATTGGGACAACTGTA
TTTGGACAAGCTGCTGCCGCTGGAGGAAGCCTATCACTTTGACAGGTTCCACTCTCCCTCGCTCTTGGAGGCCGACTTTG
ATAGCAAGCCCATGGTACTGCTCATGGGCCAGTACAGCACGGGCAAGACCACCTTTGTCAGTTACCTCCTCGAGCAGGAA
TTCCCGTGCATGCGCATTGGCCCCGAGCCCACCACGGATGGCTTCATTGTCCTCATGCATGGTGAGGTTGAGAACGTGTT
GCCAGGCAATGTGGCTGTGGTGGACAGACGCTTTCCCTTCCGCAACCTCACCAACTTCGGCAATGCCTTCCTCAACCGTT
TCGTGTGTGTCCAGCTCCCCAACGAGGTCCTGGAAAGTATCAGCATCATTGACACCCCAGGAATCCTTGCTGGAGAGAAA
CAACGGGTCAGCAGAGGTTATGATTTTGCGGGGGTCCTTCAGTGGTTTGCTGAACGAGTGGACCTTATCATCATGCTCTT
TGATGCTCATAAACTGGACATCTCGGATGAGCTCGCAGAAGCAATCCGGTCTCTCAAGAACTATGAAGACAAAATACGCG
TGGTGTTGAACAAGGCTGACCAAATAGGAACTCAGCAGCTGATGAGGGTCTATGGGGCTCTCATGTGGTCCCTGGGGAAG
ATTGTTACTGCCCCTGAAGTGATGAGGGTATATATAGGGTCCTTCTGGTCTAAGCCCTTTGTGAATGATGACAACAGCAA
GCTCTTTGAAGCAGAGGCTATGGATCTCTTTAAGGATATTCAGAAGTTGCCCCATTATACCACGATTAGAAAAATGAATG
ATTTGATTAAGCGAGCCAGACTGGCTATGGTCCATGGCTATATCATCAGCACCCTCAAGAAAGAGATGCCCATGTTTGGT
AAGGAAAGCAAAAAAAAGGAGCTGCTCAATAACTTGCAAAATGTGTACCAGAAAATTGAACGAGAATATCGTGTTTCTCC
TGGAGATTTCCCAAGCATCCCAAAGATGCAAGAACTGCTTCAGGGTCATGATTTCTCTAAGTTTCAGAACTTGAAGCCCA
AGCTCTTTGAAAACCTGGAACAGATGCTCTCCAAAGATATAGCTCGATTGATGTTTATGATAAAAGAAGAAGAGGCTGCT
GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCCCAGGCTGCTGCCATTGTGGAGGAGACCTCAGGGGCTCTGGTTATGCC
TACTGTGACACTATGA

Alignment

ORF - retro_shar_114 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.08 %
• Parental protein coverage: 74.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFSWLGHDDRRRKDPEVFQTVSEGLKKLYKTKLLPLEEYYRFHEFHSPALEDADFDNKPMVLLVGQYSTG
          MF......DRR......F..V...L..LY..KLLPLEE.Y.F..FHSP.L..ADFD.KPMVLL.GQYSTG
Retrocopy MFKSTKESDRRKS--YLFMSVAQRLGQLYLDKLLPLEEAYHFDRFHSPSLLEADFDSKPMVLLMGQYSTG

Parental  KTTFIRYLLEQDFPGMRIGPEPTTDSFIAVMQGDVEGIIPGNALVVDPKKPFRKLNAFGNAFLNRFVCAQ
          KTTF..YLLEQ.FP.MRIGPEPTTD.FI..M.G.VE...PGN..VVD...PFR.L..FGNAFLNRFVC.Q
Retrocopy KTTFVSYLLEQEFPCMRIGPEPTTDGFIVLMHGEVENVLPGNVAVVDRRFPFRNLTNFGNAFLNRFVCVQ

Parental  LPNAVLESISVIDTPGILSGEKQRISRGYDFAAVLEWFAERVDRIILLFDAHKLDISDEFSEVIKALKNH
          LPN.VLESIS.IDTPGIL.GEKQR.SRGYDFA.VL.WFAERVD.II.LFDAHKLDISDE..E.I..LKN.
Retrocopy LPNEVLESISIIDTPGILAGEKQRVSRGYDFAGVLQWFAERVDLIIMLFDAHKLDISDELAEAIRSLKNY

Parental  EDKMRVVLNKADQIETQQLMRVYGALMWSLGKIVNTPEVIRVYIGSFWSHPLLIPDNRKLFEAEELDLFR
          EDK.RVVLNKADQI.TQQLMRVYGALMWSLGKIV..PEV.RVYIGSFWS.P....DN.KLFEAE..DLF.
Retrocopy EDKIRVVLNKADQIGTQQLMRVYGALMWSLGKIVTAPEVMRVYIGSFWSKPFVNDDNSKLFEAEAMDLFK

Parental  DIQSLPRNAALRKLNDLIKRARLAKVHAYIISSLKKEMPSVFGKDNKKKELVNNLGEIYGRIEREHQISP
          DIQ.LP.....RK.NDLIKRARLA.VH.YIIS.LKKEMP..FGK..KKKEL.NNL...Y..IERE...SP
Retrocopy DIQKLPHYTTIRKMNDLIKRARLAMVHGYIISTLKKEMP-MFGKESKKKELLNNLQNVYQKIEREYRVSP

Parental  GDFPNLKKMQDQLQAQDFTKFQPLKNKLLEVVEDMLAHDIAQLMVLVRQEE
          GDFP...KMQ..LQ..DF.KFQ.LK.KL.E..E.ML..DIA.LM.....EE
Retrocopy GDFPSIPKMQELLQGHDFSKFQNLKPKLFENLEQMLSKDIARLMFMIKEEE

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_114 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
Equus caballus	ENSECAG00000015195	1 retrocopy	retro_ecab_581,
Monodelphis domestica	ENSMODG00000015505	1 retrocopy	retro_mdom_915,
Sarcophilus harrisii	ENSSHAG00000005706	1 retrocopy	retro_shar_423,
Sarcophilus harrisii	ENSSHAG00000013011	1 retrocopy	retro_shar_114 ,
Tupaia belangeri	ENSTBEG00000010371	1 retrocopy	retro_tbel_4556,