RetrogeneDB ID: retro_shar_507

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849718.1:60478..61306(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSSHAG00000006588
• Aliases: None
• Description: DDB1 and CUL4 associated factor 13 [Source:HGNC Symbol;Acc:24535]

Sequence

>retro_shar_507
ATTTTTGCTTCATGTGGGCAACAGGTGTACATCTGGGATGAATAAAAAACCAATACTATTTGTTCAATGAGTTGGGGCCT
TGACAGTATAAGCAGTGTTAAACAACCCCATTGATATCACTATCTGGGGAAGTTGTGCTTCTGACAGAAATATAGTGCTA
TATGATATGAGGCAAGCAACTCCTTTAAAAAAGGTCATCTTGGATATGAGGACAAATACAATTTGTTGGAACCCAATGGA
AGTTTTTGTTTTCATTGCAGCAAATGAAGATTATAACTTATATACATTTGATATGTGTTCCCTTGATGAACCTGTGAAGG
TACATGTGAATTATGTATCTGCAGTCCTTGGTGTGAATTACTCAGCTACAGGGAAAGAATTTGTGTCTGCTACTTTTGAC
AAATCCATTTGAATCTTCCCTATAGACAAAATCATAACACAGAGAAGCATATCATACAAAGAGAATGCAGCATGCTGTTT
TTGTGAAATGGATATCTGACAAGAAATATATTTTAAGTGGTTCTGATGAAATGAACATTTGACTCTGGAAAGCCAATGCT
TCTAAAAAAATTGATTGTGCTTACATCATGAAAAAAAGCAGCTTTAAATTATAACCAGAAGTAGAAGGAGAAGTTTAAAT
ACCATCCTCAGATAAGTCGTATAGCAAGACATTGTCATTTATCTAAGACCATCTATAGCCAAATTAAGGAGCAGCGCATC
ATGAAAGAATCTCATCAAAGGAAGTAAATGAATCATAAGAAACATAGCAAACCTGGATCTATACCATTTGTATCAGAGAA
GAAGAAGCATATAGTGGCTGTTGTGAAA

Alignment

ORF - retro_shar_507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.72 %
• Parental protein coverage: 62.02 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IFATCGQQVDIWDEQRTSPICSMTWGLDSISSVKFNPIEINILG-SCASDRNIVLYDMRQATPLKKVILD
          IFA.CGQQV.IWDE..T..ICSM.WGLDSISSVK..P.....LG.SCASDRNIVLYDMRQATPLKKVILD
Retrocopy IFASCGQQVYIWDE*KTNTICSMSWGLDSISSVK-QPH*YHYLG>SCASDRNIVLYDMRQATPLKKVILD

Parental  MRTNTICWNPMEAFVFTAANEDYNLYTFDMRSLDEPVKVHVNHVSAVLDVDYSPTGKEFVSASFDKSIRI
          MRTNTICWNPME.FVF.AANEDYNLYTFDM.SLDEPVKVHVN.VSAVL.V.YS.TGKEFVSA.FDKSI.I
Retrocopy MRTNTICWNPMEVFVFIAANEDYNLYTFDMCSLDEPVKVHVNYVSAVLGVNYSATGKEFVSATFDKSI*I

Parental  FPVDKMHS-REVYHTKRMQHVISVKWTSDNKYILCGSDEMNIRLWKANASEKLG-VLTSREKAALNYNQK
          FP.DK....RE.YHTKRMQH...VKW.SD.KYIL.GSDEMNI.LWKANAS.K...VLTS..KAALNYNQK
Retrocopy FPIDKIIT>REAYHTKRMQHAVFVKWISDKKYILSGSDEMNI*LWKANASKKID>VLTS*KKAALNYNQK

Parental  LKEKFKYHPQISRIARHRHLPKTIYSQIKEQRIMKEARQRKQMNRIKHSKPGSIPFVSEKKKHIVAVVK
          .KEKFKYHPQISRIARH.HL.KTIYSQIKEQRIMKE..QRK.MN..KHSKPGSIPFVSEKKKHIVAVVK
Retrocopy *KEKFKYHPQISRIARHCHLSKTIYSQIKEQRIMKESHQRK*MNHKKHSKPGSIPFVSEKKKHIVAVVK

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_507 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083, retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507 ,