RetrogeneDB ID: retro_shar_43

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861610.1:2074201..2075545(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000016216
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000005650
• Aliases: None
• Description: None

Sequence

>retro_shar_43
ATGGACGGCGAGTACGACGTGATCGTGCTGGGCACGGGCCTCAAGGAGTGTATCCTCTCGGGCATCATGTCCGTGAGCGG
GAAGAAGGTGCTGCACATGGACCGCAATAACTACTACGGCGGGGAGAGCGCCTCCATCACGCCCCTGCAGCAGGTGTACA
AGCACTTCGGGCTCCAGGGGCAGCCTCCCGCAAGCCTGGGCAGCGGCGCGGACTGGAACGTGGACCTGATCCCCAAATTC
CTGCTGGCCGCCGGCCAGCTGGTCAAAATGCTAGTGTACACGGAAGTGACCAATTACCTGGAATTCAAAGTGGTGGAAGG
CAGCTTTGTCTACAAAGGCGGGCAGATCTACAAGGTGCCCTCCACCGAGGCCGAGGCCTTAGCCTCCAGCCTGATGGGCG
TGCTGGAGAAAAACCAGTTTAGGAAGTTCCTCAAGTTCGTGGCGAGCTTCAACGAGGAGAACGCGGACAGCTTGGACGGC
GTCGATCCGCAGACCACCACCATGAGAGACGTGTACAAGAAGTTTGGCTTGGGCCACGATGTTATTGACTTCACAGGCCA
CGCCCTGGCCCTCTACCAGACGGACGACTACTTGGACCGGCTCTGCCCCGAGGCCATCCATCGCATCAAGCTCTACAGCA
GGTCCCTGGCTCTGTACGGGCGCAGCCCGTACTTGTACCCGCTGTACGGCCTGGGAGAGCTGCCCCAAGGGTTTGCAAGA
TTGAGTGCCATCTATGGGGGGATATACATGCTGAACAAGCCCGTGGAGGACATCGTCATGGAGAATGAAAAGGTGGTGGG
CGTGAAGTCCGAGGGGAAGGTGGTGCCCTGCAAGCAGCTCATCTGTGACCCCAGCTACGTCCCTGGCAAGGTGCGCAAGA
CGGAGCAGGTGATCCGAGTCATCTGCATCCTCAGTCACCCCATCCAGAACACGAATGACGTCAACTCGTGCCAAATCATC
ATTCCCCAGAAACAGGTCAGCAGGAGATCGGACATCTATGTGTGTATGATCTCCTCCGCCCATTATGTGGCCGCCCCGGG
AAAGTACATCGCTATCGTCAGCACCACGGTGGAAACTGCAGAGCCTGAGAAGGAGGTTGAGCCGGCGCTGAGGCTGCTGG
AACCTATAGAGCAAAAGTTTACCACCATCAGCGACATATATGAGCCCACAGATAATGGACGGGAAAGCCAGGTGTTCTGT
TCCCGTTCTTATGACGCCAGCACTGACTTTGAGACATCCTGCAATGACATCAAAGATATTTACAAGCGCATGACTGGAAC
AGACTTTAACTTTGAAAACATAAAGCGCAAAAGGAAAGATATCTTTGAAGAAGGCGAACATTGA

Alignment

ORF - retro_shar_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.59 %
• Parental protein coverage: 98.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILFSLSLSXCILSGIMSVNGKKVLHMDRNPYYGGESSSITPLEELFKRFDLPEGPPESLGRGRDWNVDLI
          I.....L..CILSGIMSV.GKKVLHMDRN.YYGGES.SITPL....K.F.L...PP.SLG.G.DWNVDLI
Retrocopy IVLGTGLKECILSGIMSVSGKKVLHMDRNNYYGGESASITPLQQVYKHFGLQGQPPASLGSGADWNVDLI

Parental  PKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVPSTETEALASNLMGMFEKRRFRKFLVFV
          PKFL.A.GQLVKML.YTEVT.YL.FKVVEGSFVYKGG.IYKVPSTE.EALAS.LMG..EK..FRKFL.FV
Retrocopy PKFLLAAGQLVKMLVYTEVTNYLEFKVVEGSFVYKGGQIYKVPSTEAEALASSLMGVLEKNQFRKFLKFV

Parental  ANFDENDPKSFEGVDPQTTTMRDVYKKFDLGQDVIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLA
          A.F.E....S..GVDPQTTTMRDVYKKF.LG.DVIDFTGHALALY.TDDYLD..C.E.I.RIKLYS.SLA
Retrocopy ASFNEENADSLDGVDPQTTTMRDVYKKFGLGHDVIDFTGHALALYQTDDYLDRLCPEAIHRIKLYSRSLA

Parental  RYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSYI
          .YG.SPYLYPLYGLGELPQGFARLSAIYGG.YMLNKPV.DI.MEN.KVVGVKSEG.V..CKQLICDPSY.
Retrocopy LYGRSPYLYPLYGLGELPQGFARLSAIYGGIYMLNKPVEDIVMENEKVVGVKSEGKVVPCKQLICDPSYV

Parental  PDRVRKAGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISYAHNVAAQGKYIAIVSTTV
          P..VRK..QVIRVICILSHPI.NTND.NSCQIIIPQ.QV.R.SDIYVCMIS.AH.VAA.GKYIAIVSTTV
Retrocopy PGKVRKTEQVIRVICILSHPIQNTNDVNSCQIIIPQKQVSRRSDIYVCMISSAHYVAAPGKYIAIVSTTV

Parental  ETGEPEKEIEPALELLEPIDQKFVAISDLYEPTDNGLESQVFCSCSYDATTHFETTCNDIKDIYKRMAGT
          ET.EPEKE.EPAL.LLEPI.QKF..ISD.YEPTDNG.ESQVFCS.SYDA.T.FET.CNDIKDIYKRM.GT
Retrocopy ETAEPEKEVEPALRLLEPIEQKFTTISDIYEPTDNGRESQVFCSRSYDASTDFETSCNDIKDIYKRMTGT

Parental  DFDFENMKRKQNDVFGEDE
          DF.FEN.KRK..D.F.E.E
Retrocopy DFNFENIKRKRKDIFEEGE

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_43 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010921	4 retrocopies	retro_meug_1228, retro_meug_2135, retro_meug_561, retro_meug_795,
Microcebus murinus	ENSMICG00000016418	1 retrocopy	retro_mmur_1095,
Sarcophilus harrisii	ENSSHAG00000005650	1 retrocopy	retro_shar_43 ,
Sarcophilus harrisii	ENSSHAG00000017568	1 retrocopy	retro_shar_127,
Tupaia belangeri	ENSTBEG00000012540	4 retrocopies	retro_tbel_1832, retro_tbel_2262, retro_tbel_2457, retro_tbel_3930,
Tursiops truncatus	ENSTTRG00000011454	1 retrocopy	retro_ttru_1205,