RetrogeneDB ID: retro_shar_754

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861939.1:59530..60972(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017836
• Aliases: None
• Description: None

Sequence

>retro_shar_754
AAGGAAGAAAGGGGAAGACCATCTGGAGATGCAAAAATAAAGGAGAAAGAAAATGTTTTTTCTAGCCTTCCTCTTATTAA
AGATGAACCAGTTGATGATGGTTATTTTGCCTCACCTAAAGAAGATATCAAGCCTTTAAAGAGACCTTGAGATGATGATA
ATGCTGATTATAAACCCAAGAAAATAAAAACAGAAGATATCAGAAAAGTGAAGAAGCGGAAACCAGAGGAAGAGGAGGAC
AACAAACAAAAATAATCAAGAACAAAGATAAGAAACTTCCTGAACCAGATAACAAGCAGAAGAAGCCCAAGAAAAAGGAG
GAGCAAAAATGGAAATGGTGGGAAGAAGAGCCCTATCCTGAAGGCATCAACTGGAAATTCCTGGAACATAAAGGCCCTGT
GTTTGCTCCACCTTACCAGCCTCTGCCAGAAAATGTCAAGTTCTACTATGATGGTAAAGTCATGAAGCTGAATCCCAAAG
CAGAAGAAGTGGCTACATTCTTTGAAAAAATGCTTGGCCATGAATACACTACTAAGGATATTTTTAGGAAAAATTTCTTC
AAAGACTGGAGAAAGGAGATGACAAATGAAGAGAAAAATAATATCACCAGTCTTAGCAAGTGTGACTTCAACCAGATAAG
CCAGTATTTCAAAGCCCAGTTGGAAGCAAGAAAGCAAATGAGCAAGGAAGAGAAACTGAAAAGCAAAGAGGAAAATGAAA
GGCTATTGAAAGAGTATGGGTTCTGTGTGATGGACAGTCACAGAGAGAGAATTGCCAACTTCAAGACTGAACCTCCAGTT
CTTTTCGAGGCACGAGGCAACCATCCCAAGATGGGAATGTTGAAAAGGCAGATTATGCCTGAAGATATAATTATCAACTG
TAGCAAAGATGCCAAGGTTCCTCCTCCTCCCCCTGGACATAAATGGAAAGAAGTTCGACATGATAACAAGGTTACCTGGC
TGGTGTCCTGGACTGAGAATATCCAAGGATACATCAAGTACATTATGCTGAACCCTAGTTCATGAATCAAGGGGGAGAAG
GTTTGGCAGAAGTATGAGACAGCCCGTATATTGAAGAAGTGCGTAGACAAGATCCAGAACCAATACCAAGAAGACTGGAA
GTCCAAGGAAATGAAAGTCCGACAGAGGGCTGTAGCATTATACTTCATTGACAAGCTTGCTCTGAGAGCTGGCAATGAGA
AAGAAGGAGAAACAGCTGATACTGTGGGCTGCTGTTCCCTCCAAGTAGAGCACATCAACTTACATCCAGAGATGGATGGC
CAGGAATACGTGGTTGAGTTTGATTTCCTAGGAAAGGATTCCATCCGATACTACAACAAGGTCCCTGTTGAGAAGAGGGT
TTTTAAGAATCTTCAGCTATTTATGGAGAACAAGCAGCCTGAGGATGATCTTTTTGATAGACTAAATAGTAGTATCCTCA
AC

Alignment

ORF - retro_shar_754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.94 %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEEKGRPSGDAKIKKEKENGFSSPPRIKDEPDDDGYFASPKEDIKPLKRPREDDDADYKPKKIKTEDIKK
          KEE.GRPSGDAKIK.EKEN.FSS.P.IKDEP.DDGYFASPKEDIKPLKRP..DD.ADYKPKKIKTEDI.K
Retrocopy KEERGRPSGDAKIK-EKENVFSSLPLIKDEPVDDGYFASPKEDIKPLKRP*DDDNADYKPKKIKTEDIRK

Parental  VKKRKPEEEEDNK-AKKIKNKDKKLPEPDNKRKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPP
          VKKRKPEEEEDNK..K.IKNKDKKLPEPDNK.KKPKK.EEQKWKWWEEE.YPEGI.WKFLEHKGPVFAPP
Retrocopy VKKRKPEEEEDNK<TKIIKNKDKKLPEPDNKQKKPKKKEEQKWKWWEEEPYPEGINWKFLEHKGPVFAPP

Parental  YEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKDIFRKNFFKDWRKEMTNEEKNNITSLSKC
          Y.PLPENVKFYYDGKVMKL.PKAEEVATFF.KML.HEYTTKDIFRKNFFKDWRKEMTNEEKNNITSLSKC
Retrocopy YQPLPENVKFYYDGKVMKLNPKAEEVATFFEKMLGHEYTTKDIFRKNFFKDWRKEMTNEEKNNITSLSKC

Parental  DFNQISQYFKAQSEARKQMSKEEKLKIKEENERLLKEYGFCVMDNHRERIANFKIEPPGLFRGRGNHPKM
          DFNQISQYFKAQ.EARKQMSKEEKLK.KEENERLLKEYGFCVMD.HRERIANFK.EPP.LF..RGNHPKM
Retrocopy DFNQISQYFKAQLEARKQMSKEEKLKSKEENERLLKEYGFCVMDSHRERIANFKTEPPVLFEARGNHPKM

Parental  GMLKRRIMPEDIIINCSKDSKVPPPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD
          GMLKR.IMPEDIIINCSKD.KVPPPPPGHKWKEVRHDNKVTWLVSWTENIQG.IKYIMLNPSS.IKGEK.
Retrocopy GMLKRQIMPEDIIINCSKDAKVPPPPPGHKWKEVRHDNKVTWLVSWTENIQGYIKYIMLNPSS*IKGEKV

Parental  WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVE
          WQKYETAR.LKKCVDKI.NQY.EDWKSKEMKVRQRAVALYFIDKLALRAGNEK.EGETADTVGCCSL.VE
Retrocopy WQKYETARILKKCVDKIQNQYQEDWKSKEMKVRQRAVALYFIDKLALRAGNEK-EGETADTVGCCSLQVE

Parental  HINLHPEMDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTSILN
          HINLHPEMDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLN.SILN
Retrocopy HINLHPEMDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNSSILN

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_754 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000017836	1 retrocopy	retro_shar_754 ,