RetrogeneDB ID: retro_shar_50

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850832.1:114615..115506(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000004651
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000013661
• Aliases: None
• Description: None

Sequence

>retro_shar_50
ATGGAGGACCAGATCCTTCATATAGCCAGGAAGTTAGATAAGTTGGTGCAGAAGAAGAACGCGGCTGGGGCCCTGGACTT
GCTAAAGGAACTTAAGAACATTCCCATGACTCTGGAATTGTTGCAGTCCACAAAAATTGGAATCTCAGTAAATACTGTTC
GCAAGCAGAGCACAGATGAAGAAGTTGCCTCATTAGCCAAGTCTCTCGTCAAATGCTGGAAGAAGTTGGTATGTGGGCCC
TCCAAGACTCAGATGAAACCACAAAAGGAACCTGCTACCTCTTCCCAAAGCAGCCCTGAGCCAGGGCAAGAAAGGAGCTC
CAGCAGCAAAGCAAAGGAAGAGACAAATGGTTCGGATTCCCTCATTAAATCATTCCCCAGGGCACCAAACACTTCAGATG
AGGTCCGAATCAAGTGCAGAGAGATGCTGGCTGCAGCCCTCAGAACTGGAGATGACTACATTGCTATTGGGGCCGATGTA
GAAGACCTGGGAGCTCAGATTGAGGAAGCTGTTTATCAGGACCTAAGGAACAAGGATATAAAGTATAAAAACAGGGTACG
AAGTAGAATAGCAAATCTCAAGGATGCAAAGAATCCAAATTTACGGAAAAACGTACTGTGTGGGAACATACCTCCAGATT
GCTTTGCTAGAATGACTGCAGAGGAAATGGCTAGTGATGAACTTAAAGAGATGCGTAAAAACCTGACCAAAGAAGCAATT
AGAACACATCAAATGGCTCAGACTGGTGGGACCCAAACTGATCTCTTCAAATGTGGCAAATGTAAAAAGAAGAATTGTAC
CTATACCCAGCTTCAAACCCTAAGTAGTGATGAACCTATGACAACATATGTTTTCTGTAATGATTGTGGACATAGATGGA
AGTTTTTTTAG

Alignment

ORF - retro_shar_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81. %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWKKLLDGPSTDKDSDEKKK
          AGALDLLKELKNIPMTLELLQST.IG.SVN..RKQSTDEEV.SLAKSL.K.WKKL..GPS..K......K
Retrocopy AGALDLLKELKNIPMTLELLQSTKIGISVNTVRKQSTDEEVASLAKSLVKCWKKLVCGPS--KTQMKPQK

Parental  ESAISSQNSPEAKEESSSSSNASNRKEETNASDSFIPSFPRAPSTSDSVRMKCREMLAAALRTGDDYIAI
          E.A.SSQ.SPE...E.SSSS.A...KEETN.SDS.I.SFPRAP.TSD.VR.KCREMLAAALRTGDDYIAI
Retrocopy EPATSSQSSPEPGQERSSSSKA---KEETNGSDSLIKSFPRAPNTSDEVRIKCREMLAAALRTGDDYIAI

Parental  GADEEELGSQIEEAIYQELRNTDMKYKNRVRSRIANLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD
          GAD.E.LG.QIEEA.YQ.LRN.D.KYKNRVRSRIANLKDAKNPNLRKNVLCGNIPPD.FARMTAEEMASD
Retrocopy GADVEDLGAQIEEAVYQDLRNKDIKYKNRVRSRIANLKDAKNPNLRKNVLCGNIPPDCFARMTAEEMASD

Parental  ELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKY
          ELKEMRKNLTKEAIR.HQMA.TGGTQTDLF.CGKCKKKNCTYTQ.QT.S.DEPMTT.V.CN.CG.RWK.
Retrocopy ELKEMRKNLTKEAIRTHQMAQTGGTQTDLFKCGKCKKKNCTYTQLQTLSSDEPMTTYVFCNDCGHRWKF

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_50 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 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50 ,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,