RetrogeneDB ID: retro_shar_49

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867597.1:129585..130641(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000004934
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009246
• Aliases: None
• Description: None

Sequence

>retro_shar_49
ATGGGCAACGCGGCCACCGCCAAGAAGGGCAGCGAGCTGGAGAGCGTGAAGGAGTTCCTGGCCAAGCCCAAGGAGGAATT
CCTCAAGAAGTGGGAAGCCCCGGCGCAGAACACGGCCCAGCTGGAGCACTTCGACCGCATCAAGACCCTGGGCACCGGCT
CGTTCGGCCGCGTGATGCTGGTGAAGCACAAGGAGACGGGCAACCACTTCGCCATGAAGATCCTGGATAAGCAGAAGGTG
GTGAAGCTGAAGCAGATCGAGCACACCCTGAACGAGAAACGCATCCTGCAGGCCGTCAACTTCCCGTTCCTGGTCCGGCT
CGAGTATTCCTTCAAGGACAACACCAACCTGTACATGGTGATGGAGTACGTGCTGGGCGGGGAGATGTTCTCCCACCTGC
GGCGCATCGGCCGCTTCAGCGAGCCCCACGCACGCTTCTATGCCGCCCAGATCGTGCTGACCTTCGAGTACCTGCACTCG
CTCGACCTGATCTACCGGGACCTGAAGCCCGAGAACCTGCTCATCGACCAGCACGGCTACATCCAGGTGACGGACTTCGG
CTTCGCCAAGCGCGTCAAAGGCCGGACCTGGACCCTGTGCGGGACCCCCGAGTACCTGGCCCCCGAGATCATCCTGAGCA
AGGGCTACAACAAGGCCGTGGACTGGTGGGCCCTGGGAGTCCTCATCTACGAGATGGCGGCGGGCTACCCCCCCTTCTTC
GCCGACCAGCCCATCCAGATCTACGAGAAGATCGTCTCCGGCAAGGTGCGCTTCCCCTCTCACTTCAGCTCCGACCTGAA
GGACCTGCTCCGCAACCTGCTCCAGGTGGACCTCACCAAGCGCTACGGCAACCTCAAGAACGGAGTCAACGACATCAAGA
ACCACAAGTGGTTCTCCACCACCGACTGGATCGCCATCTACCAGAGGAAGGTGGAAGCCCCCTTCATCCCCAAGTGCAAA
GGCCCCGGCGACACGAGTAACTTCGAAGACTACGAGGAGGAAGAGATCCGAGTCTCCATCACCGAGAAGTGCGCCAAGGA
GTTTGCCGAGTTCTAG

Alignment

ORF - retro_shar_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.98 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSFLSVKEFLAKAKEEFLKKWESPPQQSTVQLDQFDRIKTLGTGSFGRVILVKHKESGNYFAMKVLDKQK
          S...SVKEFLAK.KEEFLKKWE.P.Q..T.QL..FDRIKTLGTGSFGRV.LVKHKE.GN.FAMK.LDKQK
Retrocopy SELESVKEFLAKPKEEFLKKWEAPAQ-NTAQLEHFDRIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQK

Parental  VVKLKQIEHTMNEKRILQAINFPFLVRLEYSFKDNTNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAA
          VVKLKQIEHT.NEKRILQA.NFPFLVRLEYSFKDNTNLYMVMEYV.GGEMFSHLRRIGRFSEPHARFYAA
Retrocopy VVKLKQIEHTLNEKRILQAVNFPFLVRLEYSFKDNTNLYMVMEYVLGGEMFSHLRRIGRFSEPHARFYAA

Parental  QIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKA
          QIVLTFEYLHSLDLIYRDLKPENLLIDQ.GYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKA
Retrocopy QIVLTFEYLHSLDLIYRDLKPENLLIDQHGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKA

Parental  VDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRYGNLKNGV
          VDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRYGNLKNGV
Retrocopy VDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRYGNLKNGV

Parental  NDIKNHKWFATTDWIAIYQRKVEAPFIPKCKGPGDTSNFDDYEEEELRISITEKCAKEFADF
          NDIKNHKWF.TTDWIAIYQRKVEAPFIPKCKGPGDTSNF.DYEEEE.R.SITEKCAKEFA.F
Retrocopy NDIKNHKWFSTTDWIAIYQRKVEAPFIPKCKGPGDTSNFEDYEEEEIRVSITEKCAKEFAEF

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_49 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000072062	1 retrocopy	retro_hsap_46,
Gorilla gorilla	ENSGGOG00000013294	1 retrocopy	retro_ggor_2856,
Macropus eugenii	ENSMEUG00000002017	2 retrocopies	retro_meug_10, retro_meug_1166,
Monodelphis domestica	ENSMODG00000012087	1 retrocopy	retro_mdom_1978,
Pan troglodytes	ENSPTRG00000010585	1 retrocopy	retro_ptro_80,
Sarcophilus harrisii	ENSSHAG00000009246	2 retrocopies	retro_shar_13, retro_shar_49 ,