RetrogeneDB ID: retro_shar_91

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850208.1:50906..52745(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000003082
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000003967
• Aliases: None
• Description: None

Sequence

>retro_shar_91
ATGGAGGGTGAATTTTCAAACCCAGAGCCTGGCGTTGCGGGAGAGGAAGACTCCAAGTCTAAGAATGGGACGAATGCACA
CATTTGCTGTGTTTGCTTCCGGCCCAAGACCAATTGTTTTTTGATCAGCTGTGACAATTGCAACAAATGGTTTCATGGTA
ACTGCGTCAAGATTACAGAGAAGGTGGCCGAGGCTATACAAGAGTGGTTCTGTCTGCAGTGCCAGGAAAAGGACCCCAAA
CTGGAGCTCCGACATCAACACAAAAAAGTGTGCCATGAGCAGAATGGGGAAACTGAGGCTAAGGCGAGGGACGGTGCTGG
GACTCCGTGTCGGGAGATCGCCTCAGATCTCTTTTCAGAGTCTGTGGGAAGTGGGCCCATGACCCTCTCCAAGGACTGCG
CCTGTCCCCACAAGAAGACAACACTTGGGACTCTACAAGAAGTATCCAACCTGCAGGAAAAACGGTCAGCTCGGAGCTGT
GGGGAGCGTGAGGCTTGCCGGAGCACCGAAGATGGTGGTCACTGTGACTTCTGCCGTGACACGAAGAAATGTGGGGGGGC
CCACAAAATCCGACAAAAGTGCCAGCGCCGAGCCCGAGAATCCTATAAGCATTCCCCTTCCTCCGAAAGTCCAGAGCCGG
CTATGCGGACACCTCCGGCACCGGAAGACCATTTCCAGACGTTAAAGGAGGCGCGGGAGGCTGTGGCCCCACTCTCTCTT
GCGGAGCTGCCTCTGGACCCTGAGATCTACCCGGACTTCCCTGCTGGAGCCTTTGAGGACCACTCTTTGCCATCGTTGAG
TGACCCTGAGGATGCCCCTTTCCCGGAGCCGGTACTTCGGGATCGTGTAGTGACAGTAAAACACATCAAACGGCGGTCCG
AGACGTCCAAGAAGAAGTGCCAGCGGCAGCGGCAGAAGCAGAGGCGAAACAAGAAGCGGAAACACACGGAACCGCCAGAT
CCCGAGGACCAGGGCCCCTTGCCCCAGTGTCTGGGCCCCAACTGCGTCCGGCCTGCCCAGCCAGGCTCCAAGTACTGCTC
GGATGCCTGCGGCTTGGCGCTGGCTGCCAGTCGCATCTATGAGATCCTACCCCGGAGAATCCAGGAATGGCAGCGAAGCC
CGTGTGTGGCCGAAGAATGGGAGAAGAAACTGCTCAAGGAGATTCGAAAGGAGCAGCGGGAGGCGTGGCTGCACGTGCGG
GACGCCGAGCGTCGTTTCCAAGAGCTGGAGGATGTCATCCTCCAGGCCAAGCGACAGGTGGTCCAGGAGAACGGGGAGAA
TAATAATAAGAGATACAGCAAGCATTCAGAGCACCAGATCTTCTGCGTCTCCTGTGGTCACTCTGTCAACTCCCAGGTAG
CACTGAGGCACATGGAGCGTTGCTATGCTAAGTATGAGAGCCAGATGATCTTCGGGTCGCTGGAGCCCACGAGAATTGAG
GGGGTCTCTCGGCTCTTCTGTCAGGTATACAGCCCCCAGAGCAAAACTTACTGCAAGCGCCTGAAGGTCCTGTGCCCTGA
GCACTCCAGGGAGCCCAAGGCACCGGCAGATGAAGTGTGCGGCTGTCCCCTGGTGCGGAATGTGTTTGAGCTCACTGGAG
ACTTCTGCCGCCTGCCCAAAAGGCAGTGCAACCAGCACTACTGCTGGGAGAAGCTGCACAGGGCCGAGGTGGATCTGGAG
CAGCTGCGGGCCTGGGGCAAACTGCAGATGCTCTGGAAGCAGGAGCGAAATATCCAGATGGCAAAGGCCAACCGGGCCGG
CCTGCTGGCCCTAATGCTGCACCGGACCATCCAGCACGACCCGCTCACCTCAGACCTGCGCACCAAGCCCGACCACTGA

Alignment

ORF - retro_shar_91 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.82 %
• Parental protein coverage: 59.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKEPPEAVATPEALSDEDLPLDPELYQDFCAGAFDDHALPWLSDPEDAPFLDPALRKRAVKVKHVKRREK
          LKE..EAVA....LS...LPLDPE.Y.DF.AGAF.DH.LP.LSDPEDAPF..P.LR.R.V.VKH.KRR..
Retrocopy LKEAREAVAP---LSLAELPLDPEIYPDFPAGAFEDHSLPSLSDPEDAPFPEPVLRDRVVTVKHIKRRSE

Parental  KSEKKKEEKYKRHRQKQRHKDKWKHPERPDVKDPASLPQCLGPSCVQPAQPGSKYCSDDCGMKLAANRIY
          .S.K....K..R.RQKQR...K.KH.E.PD..D...LPQCLGP.CV.PAQPGSKYCSD.CG..LAA.RIY
Retrocopy TSKK----KCQRQRQKQRRNKKRKHTEPPDPEDQGPLPQCLGPNCVRPAQPGSKYCSDACGLALAASRIY

Parental  EILPQRIQQWQQSPCIAEEHGKKLLERIRREQQGARMRLQDMERRFHELEAVILRAKQQVVRED-EESNE
          EILP.RIQ.WQ.SPC.AEE..KKLL..IR.EQ..A.....D.ERRF.ELE.VIL.AK.QVV.E..E..N.
Retrocopy EILPRRIQEWQRSPCVAEEWEKKLLKEIRKEQREAWLHVRDAERRFQELEDVILQAKRQVVQENGENNNK

Parental  GDSEDTDLQIFCVSCGHPINPKVALRHMERCYAKYESQTSFGSMYPTRIEGATRLFCDVYNPQSKTYCKR
          ..S.....QIFCVSCGH..N..VALRHMERCYAKYESQ..FGS..PTRIEG..RLFC.VY.PQSKTYCKR
Retrocopy RYSKHSEHQIFCVSCGHSVNSQVALRHMERCYAKYESQMIFGSLEPTRIEGVSRLFCQVYSPQSKTYCKR

Parental  LQVLCPEHSRDPKVPADEVCGCPLVRDVFELTGDFCRLPKRQCNRHYCWEKLRRAEVDLERVRVWYKLDE
          L.VLCPEHSR.PK.PADEVCGCPLVR.VFELTGDFCRLPKRQCN.HYCWEKL.RAEVDLE..R.W.KL..
Retrocopy LKVLCPEHSREPKAPADEVCGCPLVRNVFELTGDFCRLPKRQCNQHYCWEKLHRAEVDLEQLRAWGKLQM

Parental  LFEQERNVRMAMTNRAGLLALMLHQTIQHDPLTTDLRTNAD
          L..QERN..MA..NRAGLLALMLH.TIQHDPLT.DLRT..D
Retrocopy LWKQERNIQMAKANRAGLLALMLHRTIQHDPLTSDLRTKPD

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_91 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010555	1 retrocopy	retro_mdom_813,
Sarcophilus harrisii	ENSSHAG00000003967	1 retrocopy	retro_shar_91 ,