RetrogeneDB ID: retro_shar_77

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861690.1:572970..573984(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000009669
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000016463
• Aliases: None
• Description: None

Sequence

>retro_shar_77
ATAGATTATCTCAAAGCAGAGATCTCTCGCAAGCGGCAGCTGGTGGAGGACAAAATGTTGCTGGAGGGAAGTAAAAGATA
CTTTAAACGGAGTGAACTTGCCAGAAAAGAAGAGGAGGCTGACTTTGGAAGATGTGCCTCCAAGATACAGCCACAAGAGA
AGGATGAGAACCAGCTAACGTCCTTCTCTCCAGTGGCAGAACTAGACCCGACAAAGGAAAAGTTGCCGATGAATCTTTCC
AGGCAAGAGATCGTGTCGCGTCTGAGAGGAAGAGGCGAACCCGTAAGATTGTTTGGAGAAACAGATTATGATGCATTTCA
GCGATTAAGAAAGATCGAGATTCTTATGCCCGAGGTTAACAAGGGTTTGAAGAATGACTTGAAGGCAGCTTTGGATAAGG
TCGAGCAACAACACTTCCAGGACATTGTTGCTGGAGAAGACACACAGAATGATCTGAAAGCCCACGAAGAAAACGCTACT
TTTGAAGAATTTGAGGCTTTGGGACAATCCTTAGGAAGGGGGGATGATTACAAAGACATGGATATCATCTCCAGGTTCCT
TAAGTTTCTCCTTAGAATTTGGACTCAAGAGCTCCAGGCTAGAGAAGAGCATGTAAAATGCAGTGTGCAGGGCAAACTGA
ACAGTGCCGCTCAGAAACAGACAGAATCCTATCTGAGGCCACTTTTCAGGAAGCTGCAAAACAGGACTCTTCCTGCAGAT
CTTAAAGAATCAATAACAGAAATTATTAAATTCATGTCACAGAGAGAATATGTGAAGGCCAACGAGGCTTATCTTCAGAT
GGCCATTGGAAATGCCCCCTGGCCAATTGGAGTCACTATGGTCGGTATCCATGCCAGAACTGGTCGTGAAAAGATCTTTT
CCAAGCATGTTGCCCACGTTCTAAATGACGAGACGCAACGAAAATTTATTCAGGGTTTAAAAAGATTAATGACCCTTTGC
CAGAAGCACTTCTCTGCATACCCATCAAAATGTGTGGAGTACAATGCACTGTGA

Alignment

ORF - retro_shar_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 56.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDTQNDLKVHEENTTIEELEALGESLGKGDDHKDMDIITKFLKFLLGVWAKELNAREDYVKRSVQGKLNS
          EDTQNDLK.HEEN.T.EE.EALG.SLG.GDD.KDMDII..FLKFLL..W..EL.ARE..VK.SVQGKLNS
Retrocopy EDTQNDLKAHEENATFEEFEALGQSLGRGDDYKDMDIISRFLKFLLRIWTQELQAREEHVKCSVQGKLNS

Parental  ATQKQTESYLRPLFRKLRKRTLPADIKESITDIIKFMLQREYVKANDAYLQMAIGNAPWPIGVTMVGIHA
          A.QKQTESYLRPLFRKL..RTLPAD.KESIT.IIKFM.QREYVKAN.AYLQMAIGNAPWPIGVTMVGIHA
Retrocopy AAQKQTESYLRPLFRKLQNRTLPADLKESITEIIKFMSQREYVKANEAYLQMAIGNAPWPIGVTMVGIHA

Parental  RTGREKIFSKHVAHVLNDETQRKYIQGLKRLMTICQKHFSTDPSKCVEYNAL
          RTGREKIFSKHVAHVLNDETQRK.IQGLKRLMT.CQKHFS..PSKCVEYNAL
Retrocopy RTGREKIFSKHVAHVLNDETQRKFIQGLKRLMTLCQKHFSAYPSKCVEYNAL

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_77 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016902	1 retrocopy	retro_mdom_166,
Otolemur garnettii	ENSOGAG00000007294	1 retrocopy	retro_ogar_1279,
Sarcophilus harrisii	ENSSHAG00000016463	1 retrocopy	retro_shar_77 ,