RetrogeneDB ID: retro_shar_22

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849899.1:671846..673847(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000010349
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017073
• Aliases: None
• Description: None

Sequence

>retro_shar_22
GCCACCGTGGTCAAGAAGTGGAAAGGCCACGTTGCGATTGACTTGGACATGGAGGACAGCAGCAGTGAGGAGAACCTGGA
TCAGGAGCTCTTGTCCCTAGCCAAACGGAAACGGAGTGACTCTGAGGAGAAGGAGCAACCTGTTAGTCAGCCTGCAGCTT
CTTCAGACTCTGAAACATCAGACGGTGATGATGACTGGACAGTTGGAGGCTCAAAAAATAAGAAAAAAGGAAAAACTGGG
AAGATAGAGCAGAAGGGAACCATGAAAAAACAGACAAACAAAGCTGCTTCCTCAGATAGCTCTGACAAAGACAGCTCAGC
TGAGAGTTCAGCCCCTGAAGAAGGTGAAGTATCTGACTCCGACAGTCACAGTTCCTTCTCCAGCTCAGATTCAGATTCTT
CTTCTGAGGATGAGGAATTCCATGATGGATATGGAGAAGACCTCATGGGAGATGAAGAAAATAGGGCCCGTTTAGAACAA
ATGACAGAGAAGGAGAGAGAACAGGAACTGTTTAACAGGATAGAAAAGAGAGAGATGCTGCAAAGAAGGTATGAAATTAA
GAAGAAATTAAAAACAGCCAAGAAGAAAGAAAAAAAGAAAAAACAAGAAGAACAAGAGAAGAAAAAATTTACACAAATTC
AAGAGTCCCAGGTCATGTCCCATAATAAGGAGCGACATTGCAAGTGGGATGAAAAACTAGACAAAAAATCTCAGGCCATG
GAAGAACTGAAAGCAGAGAGAGAAAAACGGAAGAATAGAACAGCTGAGCTGCTTGCCAAAAAACAACCATTAAAAACAAG
TGAAGTTTACTCTGATGATGAAGAGGAGGACGATAAGTCCAGTGAGAAGACAGATTATTCATCTAGTACGACATCATCTG
ATGAAGAGGAGGAAAAGGAAGAGGTTCCTCCAAAATCACAGCCAGTTTCTCTGCCTGAAGATTTGAACCGAGTGCGGTTA
TCTCGGCACAAGCTGGAACGGTGGTGTCACATGCCTTTCTTTGCTAAGACAGTCATAGGATGTTTTGTACGAATTGGCAT
TGGGAACTACAACAGTAAGCCTGTCTATCAGGTGGCTGAAATCACTAGTGTGGTGGAAACAGCCAAGGTTTATCAGTTGG
GTGGCACAAGGACAAATAAAGGATTGCAGTTGAGGTATGGCAATGACCAGCTAGTATTCCGCTTGGAGTTTGTCTCAAAC
CAAGAGTTCACAAAAAGTGAATTTATGAAATGGAAAGAAGTGATGTTTTCTGCCGGCATGCAGCTACCTACCTTGGATGA
AATCAACAAGAAGGAAGTATCCATTAAAGAAGCTTTGAATTATAAATTCAATGATCAGGATATTGAAAAGATTGTAAAAG
AGAAAGAGAGATTCAGAAAAGCTCCACCCAACTATGCCATGAAAAAAATGCAGCTTCTGAAGGAGAAGGCCATGGCAGAA
GATGTGGGAGACCAAGACAAGGCTAAACAAATCCAACATCAACTGAATGAGTTGGAGGAAAGGGCAGAGGCCCTAGATCG
GCAACGAACAAAGAATATTTCTGCCATCAATTACATCAACCAACGAAATCGGGAATGGAACATAGTTGAGTCTCAGAAAG
CCCTTGTGGCTGAAAATCACAACATGAAAAATCAAAAGATGGATCCCTTCATTAGGCGGCATTGCAAACCAACTATTGTC
TCCAATTCCAGAAACCCTGCTGTTCAAGCTGCCAGGCTGGCTCAGCTGAATGCAAAATATGGCTCTGGGGCATTACCAGA
TGCTCCAAAGGAGATGAACAAGGGTCAAGGAAGAGACAAAGACGCCAACTCTAAGTCAGCCAGTGATCTCTCAGAGGACC
TGTTCAAAGTGCATGATTTTGATGTGAAGATCGACTTCCAAGTTCCCAGTTCAGAATCAAAGACACTGGCCATCACCTCA
AAGGCTCCCCCAGCCAAGGATGGTGCTCCAAGAAGGTCTCTGAATTTAGAAGATTATAAGAAACGACGAGGATTTATTTG
A

Alignment

ORF - retro_shar_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELLSLAKRKRSDSEEKEQPVSQPAASSDSETSDSDDEWTVGGSKNKKKGKTGKIEKKGTMKKQTNKAASS
          ELLSLAKRKRSDSEEKEQPVSQPAASSDSETSD.DD.WTVGGSKNKKKGKTGKIE.KGTMKKQTNKAASS
Retrocopy ELLSLAKRKRSDSEEKEQPVSQPAASSDSETSDGDDDWTVGGSKNKKKGKTGKIEQKGTMKKQTNKAASS

Parental  GSSDKDSSAESSAPEEGEVSDSDSNSSSSSSDSDSSSEDEEFHDGYGEDLMGDEEDRARLEQMTEKEREQ
          .SSDKDSSAESSAPEEGEVSDSDS.SS.SSSDSDSSSEDEEFHDGYGEDLMGDEE.RARLEQMTEKEREQ
Retrocopy DSSDKDSSAESSAPEEGEVSDSDSHSSFSSSDSDSSSEDEEFHDGYGEDLMGDEENRARLEQMTEKEREQ

Parental  ELFNRIEKREVLKRRFEIKKKLKTAKKKEKKEKKKKQEEEQEKKKLTQIQESQVMSHNKERRSKRDEKLD
          ELFNRIEKRE.L.RR.EIKKKLKTAKKKE....KKK..EEQEKKK.TQIQESQVMSHNKER..K.DEKLD
Retrocopy ELFNRIEKREMLQRRYEIKKKLKTAKKKE----KKKKQEEQEKKKFTQIQESQVMSHNKERHCKWDEKLD

Parental  KKSQAMEELKAEREKRKNRTAELLAKKQPLKTSEVYSDDEEEEEDDKSSEKTDRSSRTTSSDEEEEKEEV
          KKSQAMEELKAEREKRKNRTAELLAKKQPLKTSEVYSDDEEE..DDKSSEKTD.SS.TTSSDEEEEKEEV
Retrocopy KKSQAMEELKAEREKRKNRTAELLAKKQPLKTSEVYSDDEEE--DDKSSEKTDYSSSTTSSDEEEEKEEV

Parental  PPKSQPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQ
          PPKSQPVSLPE.LNRVRLSRHKLERWCHMPFFAKTV.GCFVRIGIGN.NSKPVY.VAEIT.VVETAKVYQ
Retrocopy PPKSQPVSLPEDLNRVRLSRHKLERWCHMPFFAKTVIGCFVRIGIGNYNSKPVYQVAEITSVVETAKVYQ

Parental  LGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKEVSIKEALNYK
          LGGTRTNKGLQLR.GNDQ.VFRLEFVSNQEFT.SEFMKWKE.MFSAGMQLPTLDEINKKEVSIKEALNYK
Retrocopy LGGTRTNKGLQLRYGNDQLVFRLEFVSNQEFTKSEFMKWKEVMFSAGMQLPTLDEINKKEVSIKEALNYK

Parental  FNDQDIEEIVKEKERFRKAPPNYAMKKTQLLKEKAMAEDLGDQDKAKQIQDQLNELEERAEALDRQRTKN
          FNDQDIE.IVKEKERFRKAPPNYAMKK.QLLKEKAMAED.GDQDKAKQIQ.QLNELEERAEALDRQRTKN
Retrocopy FNDQDIEKIVKEKERFRKAPPNYAMKKMQLLKEKAMAEDVGDQDKAKQIQHQLNELEERAEALDRQRTKN

Parental  ISAISYINQRNREWNIVESEKALVAESHNMKNQQMDPFTRRQCKPTIVSNSRDPAVQAAILAQLNAKYGS
          ISAI.YINQRNREWNIVES.KALVAE.HNMKNQ.MDPF.RR.CKPTIVSNSR.PAVQAA.LAQLNAKYGS
Retrocopy ISAINYINQRNREWNIVESQKALVAENHNMKNQKMDPFIRRHCKPTIVSNSRNPAVQAARLAQLNAKYGS

Parental  GALPDAPKEMNKGQGKDKDINSKSASDLSEDLFKVHDFDVKIDLQVPSSESKTLAITSKAPPAKDGAPRR
          GALPDAPKEMNKGQG.DKD.NSKSASDLSEDLFKVHDFDVKID.QVPSSESKTLAITSKAPPAKDGAPRR
Retrocopy GALPDAPKEMNKGQGRDKDANSKSASDLSEDLFKVHDFDVKIDFQVPSSESKTLAITSKAPPAKDGAPRR

Parental  SLNLEDYKKRRGLI
          SLNLEDYKKRRG.I
Retrocopy SLNLEDYKKRRGFI

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_22 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000016112	1 retrocopy	retro_mluc_588,
Sarcophilus harrisii	ENSSHAG00000017073	2 retrocopies	retro_shar_22 , retro_shar_345,