RetrogeneDB ID: retro_shar_432

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842598.1:40933..41598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000016459
• Aliases: None
• Description: None

Sequence

>retro_shar_432
TACAAACCTTCAGATGAATATAAGACTGATGCTCTTAACCCTGACAATCTGCAGGGTGGTGATTACTTGGATTCTAACTA
TGTGTTGAGTTCTCATATTTCAACTGGCTGAACTATTTGGGGATTCTACCTGCCTCCAATTATAGCTGGAGTGAGTGCTG
TGTCATAGAGAAGCTCTCTATGGAAACTCTGGTCAACCTGGAATGTGACCTGAATAGGAAGTACTATGCTTTGAAGAACA
TAACTGAGTAGGAACAGTAGCAGCTGTTTGATGACCACTTCCCTCTTCAACAAGCCTGCCTCTCCCTTTCTCTTGGCATC
TGGCATGGCCTGAGACTGGCCTGATGGCAGGGGCATTTGATACAATGCCAACAAAATCTTTCTGGTGTGGATCATTGAGG
AAGATCACCTGAGAGTTATCTCCACAAGAAGGAAGGTAACATGAAGGAAGTGTTCACACATTTCTACATGAGGCTCACCC
AGACTGAAATCCTTTTTCATATCAAGAACTACAAGTTCATTTGGAATCCCCACTTGGGCTACATCCTGACCTGCCCCTAC
AATCTGGTCACAACCCTATATGCAGTTGAACACATCAAACTGCCCCACCTGGGCAAGGATGAGTAGTTTGGTGAGGTGTT
GAAGAAAGTGATGCTCCAGAAAAGG

Alignment

ORF - retro_shar_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 58.01 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YKPSDEHKTD-LNPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPP-HCSRGERRAIEKLSVEALASLEG
          YKPSDE.KTD.LNPDNLQGGD.LD.NYVLSS...TG..I.GF.LPP...S..E...IEKLS.E.L..LE.
Retrocopy YKPSDEYKTDALNPDNLQGGDYLDSNYVLSSHISTG*TIWGFYLPP<NYSWSECCVIEKLSMETLVNLEC

Parental  DLNGKYYALKNMTEQEQQQLIDDHF-LFDKPVSPLLLASGMARDWPDGRGIWHNDNKTFLVWINEEDHLR
          DLN.KYYALKN.TE.EQ.QL.DDHF.LF.KP.SP.LLASGMA.DWPDGRGI..N.NK.FLVWI.EEDHLR
Retrocopy DLNRKYYALKNITE*EQ*QLFDDHF>LFNKPASPFLLASGMA*DWPDGRGI*YNANKIFLVWIIEEDHLR

Parental  VISMQ-KGGNMKEVFTRFCTGLTQIESLFKTKNYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPHLGKY
          VIS...K.GNMKEVFT.F...LTQ.E.LF..KNY.F.WNPHLGYILTCP.NL.T.L.A..HIKLPHLGK.
Retrocopy VISTR<KEGNMKEVFTHFYMRLTQTEILFHIKNYKFIWNPHLGYILTCPYNLVTTLYAVEHIKLPHLGKD

Parental  EKFGEVLKKLRLQKR
          E.FGEVLKK..LQKR
Retrocopy E*FGEVLKKVMLQKR

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_432 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 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018277	5 retrocopies	retro_cfam_1828, retro_cfam_2061, retro_cfam_2159, retro_cfam_274, retro_cfam_664,
Ciona intestinalis	ENSCING00000007141	1 retrocopy	retro_cint_27,
Echinops telfairi	ENSETEG00000008667	1 retrocopy	retro_etel_1667,
Macropus eugenii	ENSMEUG00000002979	3 retrocopies	retro_meug_1069, retro_meug_1569, retro_meug_2156,
Mus musculus	ENSMUSG00000001270	4 retrocopies	retro_mmus_1460, retro_mmus_1578, retro_mmus_1647, retro_mmus_2390,
Oryctolagus cuniculus	ENSOCUG00000008818	1 retrocopy	retro_ocun_1562,
Sarcophilus harrisii	ENSSHAG00000016459	2 retrocopies	retro_shar_432 , retro_shar_645,