RetrogeneDB ID: retro_shar_1

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861705.1:3483916..3485047(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000018334
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000008796
• Aliases: None
• Description: None

Sequence

>retro_shar_1
ATGAGCGCGCTCAGACTCCCCGGGATGTCTGCCGTCGTCCTCTCGGTCTTCGGCTTGGTCTTCATCTGCAGCGGCCTGGT
CGTCAACGTCCTCCAGCTGGCCTCCCTCGTTTTCTGGCCTCTCAGTAGGAAGTTCTACCGCAAGGTCAACAGTTTCCTCG
GCTACTCCCTCTATTGCCATCTAATCACGCTGCTGACGTGGTGGTCGGGCTCCGAATGCACCTTATTCACGGAGCGGGAT
TCCCTGGGCAAGTTAGGGAAGGAGACCGCCATCATCATCTTTAATCACACCTTTGAGATCGACCTTCTCTGTCTCTGGAC
CTTATGTGATCGCTATGGGATCCTGGGGACTTTGAAGGCAATGGCCAAAAAAGAGCTCCTCTGGGTGCCTGTGATTGGCT
GGACGCCGTACTTTCTGGAAAGCGTGTTCTGCGAGAGGAAATGGGAGCACGACCAGGCGGGGCTCGTTAAAAGCCTGGGC
CGTTTGGCCGACTTCCCGGAGCCCTTTGGCTTTGTCGTGTTCTGCGAAGGGACTCGCTTCACGCAGGAAAAGCATCGCGT
CAGTATGGAGGTGGCCCGAGCCAAGGGGCTGCCCCGGCTCAAGTACCACCTGCTGCCCAGGACCAGGGGCTTCGCCGTCG
CCGTCCGCTGCCTGCGCGGGCGAGCCTCCGCGGTCTATGACGTCACGCTCAATTTCCGAGGCCGTCGCTACCCAACTTTG
CTGGGGCTCATTCGGAGGGAGAAGCACCAAGCGGACATGTGCTTTAGGAGAATTCCTTTGGAGGAGGTCCCGCTGGAGGA
GCAGGAGATCGCCCCCTGGCTCCATCGGCTGTACCAGGAGAAGGATGCTCTGCAGGAATTCTACAACCAGAGCGGGACGT
TTCCAGGAGAACGGGTTAAGCTCGGCAGAAGACTGTGGGCTCCCTTGCATTTCTCCTTTTGGGCTGTTGTCGTCCTATTT
GCTCTCTTCAAGGTGGCAGTTAGCATTTTTCTAAGTGGATCCCCCCTGCTGATAGCGACATTCTTTGGATTTTGGGGGGG
AACTGTTTTTGGAATTCACATACTGGTAGGAGTCACTAAAATAGAAAATGCTTCTGCCTATGGAAACCAAGAATTCCAGA
AAAGGGAATAA

Alignment

ORF - retro_shar_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.4 %
• Parental protein coverage: 97.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVHLLIGFVFVVSGLIINFIQLFTLLLWPINKQFYRKVNCRLSYSLWSQLVMLLEWWSGTECTLFTDQET
          VV....G.VF..SGL..N..QL..L..WP....FYRKVN..L.YSL...L..LL.WWSG.ECTLFT....
Retrocopy VVLSVFGLVFICSGLVVNVLQLASLVFWPLSRKFYRKVNSFLGYSLYCHLITLLTWWSGSECTLFTERDS

Parental  VAKFGKEHVVIILNHNFEIDFLCGWTMCERFGVLGSSKVLAKKELLYVPLIGWTWYFLEIVFCKRKWEED
          ..K.GKE...II.NH.FEID.LC.WT.C.R.G.LG..K..AKKELL.VP.IGWT.YFLE.VFC.RKWE.D
Retrocopy LGKLGKETAIIIFNHTFEIDLLCLWTLCDRYGILGTLKAMAKKELLWVPVIGWTPYFLESVFCERKWEHD

Parental  RDTVIEGLKRLSDYPEYMWFLLYCEGTRFTETKHRISMEVAESKGLPKLKYHLLPRTKGFTTAVQCLRGT
          .......L.RL.D.PE...F...CEGTRFT..KHR.SMEVA..KGLP.LKYHLLPRT.GF..AV.CLRG.
Retrocopy QAGLVKSLGRLADFPEPFGFVVFCEGTRFTQEKHRVSMEVARAKGLPRLKYHLLPRTRGFAVAVRCLRGR

Parental  ATVAAVYDVTLNFRGNKNPSLLGILYGKKYEADMCVRRFPLEDIPQDEKEAAKWLHKLYQEKDALQELYK
          A...AVYDVTLNFRG...P.LLG.....K..ADMC.RR.PLE..P..E.E.A.WLH.LYQEKDALQE.Y.
Retrocopy A--SAVYDVTLNFRGRRYPTLLGLIRREKHQADMCFRRIPLEEVPLEEQEIAPWLHRLYQEKDALQEFYN

Parental  QKGVFPGEQIKPIRRPWTLLNFLGWATILLSPLFSFAFGVFASGSPLLILTFLGFVGAASFGVRRLIGVT
          Q.G.FPGE..K..RR.W..L.F..WA...L..LF..A...F.SGSPLLI.TF.GF.G...FG...L.GVT
Retrocopy QSGTFPGERVKLGRRLWAPLHFSFWAVVVLFALFKVAVSIFLSGSPLLIATFFGFWGGTVFGIHILVGVT

Parental  EIEKGSSYGNQEFKKKE
          .IE..S.YGNQEF.K.E
Retrocopy KIENASAYGNQEFQKRE

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_1 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000004785	2 retrocopies	retro_mluc_1325, retro_mluc_2271,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687,
Sarcophilus harrisii	ENSSHAG00000008796	1 retrocopy	retro_shar_1 ,