RetrogeneDB ID: retro_shar_54

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867621.1:2184767..2186492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000016470
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017769
• Aliases: None
• Description: None

Sequence

>retro_shar_54
ATGTTCGCCAAGTCCTTCCGTGTCAAGTCAAACGCTGCCATCAAGGGCTCTGACAGGCGCAGGCTTCAGGCCGACGTGGC
CGTCACTTTTCCGGACGTTGACAGAGAACGGATTCCTGGGAGGAAAGAGCTCAGCATCATGAGACTCTGCCTTTACAAAG
GAAACGCCGCGACTGTATATGTGAGTGGGAGAAACCCTGTTTTTTTTGAAGTAGAGAAAAACCTGTATCCAACCGTTTAC
ACTCTCTGGGCCTACCCCGATCTTTTGCCGGCCTTCACAACATGGCCGACCGTGCTGAGAAAGTTGGCAGGAGGAGCGGA
TTTCCTGCTGCCGGAGATCGTGGTACCCTCCGGCGGCCTGCCTGTGGTAAAGCAGGGGGATCTCTGCGCCATCGCTTTGG
TTGGGAACAGGGCTCCGGTGGCCATCGCGGTAGCCAAAATGTCCTCCGCTGAGATGCTGGCCTCTGATCTCAAGGGGAAA
GGCTTCACTGTGCTCCACACCTACCTCGACTGTTTGTGGCACATAGGCGATAGGTCATCCCCGCCCACCGTCATCCCGTT
GGACCGGGTTCCTCCGGAGCTCGAGGAGAATGCCAGAGAGGAGGGGGCGGCCCGGGGGAACCCTGTTGTTCGGGAACAGG
TGCGACGGGGGAAGGGAATCAGGGTGGCACGAGAGAATCCTCCCGTAGAAGCCGCGGAGGGCTCTGGTGTGGCAGAATCG
AGTCAGGCCTCCACCAGCGATAAGAGCCTTCAAGAGCAGATGGATGAGCTGCTGCGTAATTGTTTTTTTCACGCGCTGAA
GAGCCGGGTCACCGAGGCCGACCTGCCCTTGCTCACTAGCACCTTTCTGGGTAGCCACATGTTTTCCTGCTGCCCCAGAG
GGCAACAGCTGGACATGAAAAAGTCGAGCTACAGAAAGCTCTCCAAATTCCTGCACCAGATGATGAAGCAGCAGATCCTG
CAGTTGAAGGAGCTGAGCAAAGGGGTAGAAAGCATTGTGTCCGTGGACTGGAAGCACCCCAGTATCACCTCTTTTATCGT
GCCCAAGCCGGCTCCAGACTATCGGGTCGCCCAGAAGGTTAGGCAGGGGGAACGGTCCTATTATGCTCCAGAGATCAAAT
CCCTGTACTGCGTCCCAGCCAGGATGTCTGCTCTTTTCCAAGACTCCGGCTTCAAGAGAGGGAGCATCCTCTCTGCCCGT
GAGGTCCGCAGGACCCTCTGGGACTACGTCCAGAGGAACAAGCTGGTTGATGCAGAGTGCAAAGACTTTGTTAAGTTGGA
TTCCATCTTGTGCGACTGCCTCCTGGGGAAATCGGAGCAGTTCAACCTGGACAGACTTCCGTGGGATAATCTCTTTGCAA
GATGCCTGGGGAGACTGCAGTCTGCCTATAAAGTGACTTTTTATGGACAAGAGCCCGTTGTGAAGAAAGGAAAAATATAT
CCTATTGAAATCATCCTGGCGCAGCGAGCATTCAACAAAAAAGTCACCCTGATCCGGAATCTGAAGACCTATGGACTGGA
TCCTTATGATGTAGCTGCTCTTCTTAAGCAACGTGGCCAGACCAGTGCCACGGTCAGCCAGATCCCTCAAGACAGGAATG
CTGTTCAAGTCCAAATCCAAGGCAACCAGATCAGTCTTCTCAGTCATCTCCTGCTTGAAGAATATTGTATCCCTGCAAAA
TACATCTATGGCCTGGAAAAAGCTTTCAGAGCTTACAAGAACTGA

Alignment

ORF - retro_shar_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.86 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFAKAFRVKSNTAVKGSDRRKLRTDVAAAFPAFGSEQLSELVPGKEELNAVKLYAHKGDAVTVYVNGSNP
          MFAK.FRVKSN.A.KGSDRR.L..DVA..FP....E......PG..EL....L...KG.A.TVYV.G.NP
Retrocopy MFAKSFRVKSNAAIKGSDRRRLQADVAVTFPDVDRERI----PGRKELSIMRLCLYKGNAATVYVSGRNP

Parental  ILFELRGTLYPTVYTLWSYPNLLPAFTTWPPVLEKLVGGADLMLPGLTVPPGGLPQVQQGDLCAITLVGN
          ..FE....LYPTVYTLW.YP.LLPAFTTWP.VL.KL.GGAD..LP...VP.GGLP.V.QGDLCAI.LVGN
Retrocopy VFFEVEKNLYPTVYTLWAYPDLLPAFTTWPTVLRKLAGGADFLLPEIVVPSGGLPVVKQGDLCAIALVGN

Parental  RAPVAVGVAIMSTAEMLASGLKGRGFTVLHTYLDHLWQFGDKSSPPSIAPLDQDPSKCVGNPKEEGPVQV
          RAPVA..VA.MS.AEMLAS.LKG.GFTVLHTYLD.LW..GD.SSPP...PLD..P.....N..EEG....
Retrocopy RAPVAIAVAKMSSAEMLASDLKGKGFTVLHTYLDCLWHIGDRSSPPTVIPLDRVPPELEENAREEGAARG

Parental  DSILQDNLEHLTLQGDEESRVARPTSSSEAAEELGETEMDQDSTDTKTLQEQMDELLLRCFFHALKCRVT
          ..............G....R...P....E.....G..E..Q.ST..K.LQEQMDELL..CFFHALK.RVT
Retrocopy NPVVREQVRR--GKGIRVARENPPVEAAEGS---GVAESSQASTSDKSLQEQMDELLRNCFFHALKSRVT

Parental  KADLPLLTSTFLGSHMFSCCPEGQQLDIKKSSYKKLSKFLHHMVKEEIVQVKELSKGVESIVAVNWKHPS
          .ADLPLLTSTFLGSHMFSCCP.GQQLD.KKSSY.KLSKFLH.M.K..I.Q.KELSKGVESIV.V.WKHPS
Retrocopy EADLPLLTSTFLGSHMFSCCPRGQQLDMKKSSYRKLSKFLHQMMKQQILQLKELSKGVESIVSVDWKHPS

Parental  ITSFVVPESSPAAQSVQEDTK-EKPYRAPDIRSLYCIPANMTSLFQASGHKKGNTLSGNEVREIIIDYAK
          ITSF.VP...P.....Q.....E..Y.AP.I.SLYC.PA.M..LFQ.SG.K.G..LS..EVR....DY..
Retrocopy ITSFIVPKPAPDYRVAQKVRQGERSYYAPEIKSLYCVPARMSALFQDSGFKRGSILSAREVRRTLWDYVQ

Parental  KNNLVDANNKNLVKLDPILCDCILEKDEQYTILMLPWDKLIERCLERLKPAYEVTFYGQEPIVKKGKICP
          .N.LVDA..K..VKLD.ILCDC.L.K.EQ.....LPWD.L..RCL.RL..AY.VTFYGQEP.VKKGKI.P
Retrocopy RNKLVDAECKDFVKLDSILCDCLLGKSEQFNLDRLPWDNLFARCLGRLQSAYKVTFYGQEPVVKKGKIYP

Parental  IEITLAHRTYNKKVTLIQNLEVFGLDPYSVASILQQRCQASATITPVPGSKDAIQVQIQGNQINHLSRLL
          IEI.LA.R..NKKVTLI.NL...GLDPY.VA..L.QR.Q.SAT....P....A.QVQIQGNQI..LS.LL
Retrocopy IEIILAQRAFNKKVTLIRNLKTYGLDPYDVAALLKQRGQTSATVSQIPQDRNAVQVQIQGNQISLLSHLL

Parental  LEEYDIPRKYIHGLEKAPKAGK
          LEEY.IP.KYI.GLEKA..A.K
Retrocopy LEEYCIPAKYIYGLEKAFRAYK

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_54 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000008777	1 retrocopy	retro_meug_1854,
Myotis lucifugus	ENSMLUG00000001410	1 retrocopy	retro_mluc_63,
Monodelphis domestica	ENSMODG00000002070	1 retrocopy	retro_mdom_2028,
Sarcophilus harrisii	ENSSHAG00000017769	1 retrocopy	retro_shar_54 ,