RetrogeneDB ID: retro_shar_290

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841235.1:2435605..2436479(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1
• Ensembl ID: ENSSHAG00000007685
• Aliases: None
• Description: cyclin B1 [Source:HGNC Symbol;Acc:1579]

Sequence

>retro_shar_290
TTGAAGGGCAATGTCCCAGTTACCAAGAGGGTGACTGTTTCCACTGCTGCCTCCAAGCTTGGGCTGAAGCTAAAAATGAC
CCTTGGTGATATTGGCATCAAAATGTGTGAGGAACAGCAGTCATCTCCATCTAAAATACCTCTGAAAAAGGAAATCAAGT
TCTAATAGTAAAAGCAGCTGATAAAAAAGCCTCCCAATCCATTAGAAAAGATTCCTCTTCCTAAAATCGTTAAGGAAGAG
AAACTAACTTGTGAACTCATTAGGCTGGATTCTCCATCTCTAAGCCCAATGGAAACATCTGGGTCTGTGTCTACAGAAGA
GTTTCTGTGCCAAACTTTTTTCCAGTGTCATACTTGGACTGAAAGATTTTGAATTCCAAAGATACAGCTGATCCAAAACT
TCGTAGTAAAGATGTGAAAGATGTGCATTGCTATTTCAGACAACTTGAGGAAGAGCACATGATTAGACCAATATACCTGG
TGGGTCAAGAAGCCACTGGGAACAAAACAGCCATCCTAATTGACTGGTGGGTAAAAGCACAGATGAATTTTACGTTGCTA
TAGGAGACTATCTACATGACAGTGGCCATTATTAACTGATTTATGCAGGATAATAGTGTGTCTAAAAAACTGTGGGAGTT
GGTGGGTGTTATCCCCATGTTCATTGTCACCAATTATGAAGTGATGTGCCCACCTGAAATTGGAAACCTCGCCTTTGTAA
TTGGCCATATTGCAGAAAGCACCAGATTCAGTAGATGAAAATGAAGATTCTAAAAATTTTAGACTTAAGTGTAGGTTGTC
CTTTACCACTATACCTTCTATGCTAAATAGCTAATGTAGTAGGAATTAACATTGAATAGCACACTTCAGTTAAG

Alignment

ORF - retro_shar_290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.68 %
• Parental protein coverage: 70.02 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKGNNVPGAKRVPVPSAASKPGLRPRMALGDIGNKVCEQQQAPPSKIPLKKETKAPISKVAAKKAPKPVE
          LKGN.VP..KRV.V..AASK.GL...M.LGDIG.K.CE.QQ..PSKIPLKKE.K....K...KK.P.P.E
Retrocopy LKGN-VPVTKRVTVSTAASKLGLKLKMTLGDIGIKMCEEQQSSPSKIPLKKEIKF***KQLIKKPPNPLE

Parental  KMPVPEPVKEEKITPEPIKVDSPSPSPMETSGCAPAEEYLCQAF-SDVLLAVKD-VDAEDNADPNLCSEY
          K.P.P..VKEEK.T.E.I..DSPS.SPMETSG....EE.LCQ.F.S.V.L..KD.....D.ADP.L.S..
Retrocopy KIPLPKIVKEEKLTCELIRLDSPSLSPMETSGSVSTEEFLCQTF>SSVILGLKD>LNSKDTADPKLRSKD

Parental  VKDIYCYLRQLEEEQAVRPKYLVGQEVTGNMRAILIDWLVQVQMKFRLLQETMYMTVAIIDRFMQDNSVP
          VKD..CY.RQLEEE...RP.YLVGQE.TGN..AILIDW.V..QM.F.LL.ET.YMTVAII..FMQDNSV.
Retrocopy VKDVHCYFRQLEEEHMIRPIYLVGQEATGNKTAILIDWWVKAQMNFTLL*ETIYMTVAIIN*FMQDNSVS

Parental  KKLLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDHTYS-KHQIRQMEMKILKALDFSLGRPLPLHFLRRA
          KKL..LVGV..MFI...YE.M.PPEIG..AFV..H....KHQI..M.MKILK.LD.S.G.PLPL..L...
Retrocopy KKLWELVGVIPMFIVTNYEVMCPPEIGNLAFVIGHIAE<KHQIQ*MKMKILKILDLSVGCPLPLYLLC*I

Parental  SKVGEVDIEQHTLAK
          ..V....IE.HT..K
Retrocopy ANVVGINIE*HTSVK

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_290 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 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Myotis lucifugus	ENSMLUG00000012856	1 retrocopy	retro_mluc_1020,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290 ,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,
Tursiops truncatus	ENSTTRG00000002874	2 retrocopies	retro_ttru_524, retro_ttru_59,