RetrogeneDB ID: retro_shar_308

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841295.1:953345..953604(-)
• Located in intron of: ENSSHAG00000011872

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO3
• Ensembl ID: ENSSHAG00000002220
• Aliases: None
• Description: small ubiquitin-like modifier 3 [Source:HGNC Symbol;Acc:11124]

Sequence

>retro_shar_308
AAGGAAAGAGTCAAGACTGAAAATAATAACCACATTAATTTGAAGGTGATAGGGCAACTTGAATCAGTGTGCAATTTAAA
ATTAAGAGACACATACCATTGAGTAAACTACTGAAAACATATCGTGAATGACAGGCTTTGTCAATGAGGCAGATCAGATT
CCATTTGATGGACAACCAATCAATGAAACAGACACCCCTGCACAATTGGAAATGGAGGATGAAGATACAGTTGATGTATT
CCCTAATCAGACAAGGGGC

Alignment

ORF - retro_shar_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.4 %
• Parental protein coverage: 92.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEGVKTEND-HINLKVAGQDGSV-VQFKIKRHTPLNKLMKAYCERQGLSMRQIRFR-FDGQPINETDTPA
          .E.VKTEN..HINLKV.GQ..SV.VQFKIKRH.PL.KL.K.Y.E.Q.LSMRQIRF..FDGQPINETDTPA
Retrocopy KERVKTENNNHINLKVIGQLESV<VQFKIKRHIPLSKLLKTYRE*QALSMRQIRFH<FDGQPINETDTPA

Parental  QLEMEDEDTIDVFQQQTGG
          QLEMEDEDT.DVF..QT.G
Retrocopy QLEMEDEDTVDVFPNQTRG

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_308 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 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017321	3 retrocopies	retro_btau_1730, retro_btau_580, retro_btau_701,
Bos taurus	ENSBTAG00000030169	8 retrocopies	retro_btau_1047, retro_btau_1484, retro_btau_1804, retro_btau_260, retro_btau_344, retro_btau_489, retro_btau_582, retro_btau_895,
Felis catus	ENSFCAG00000026550	4 retrocopies	retro_fcat_1210, retro_fcat_1947, retro_fcat_823, retro_fcat_836,
Myotis lucifugus	ENSMLUG00000025342	4 retrocopies	retro_mluc_1502, retro_mluc_272, retro_mluc_340, retro_mluc_625,
Myotis lucifugus	ENSMLUG00000028601	2 retrocopies	retro_mluc_1321, retro_mluc_2494,
Macaca mulatta	ENSMMUG00000006760	3 retrocopies	retro_mmul_2131, retro_mmul_2215, retro_mmul_47,
Mustela putorius furo	ENSMPUG00000010234	1 retrocopy	retro_mputfur_1504,
Mustela putorius furo	ENSMPUG00000013954	9 retrocopies	retro_mputfur_1086, retro_mputfur_1403, retro_mputfur_1535, retro_mputfur_273, retro_mputfur_275, retro_mputfur_385, retro_mputfur_666, retro_mputfur_948, retro_mputfur_995,
Oryctolagus cuniculus	ENSOCUG00000021739	4 retrocopies	retro_ocun_1024, retro_ocun_1631, retro_ocun_1690, retro_ocun_321,
Rattus norvegicus	ENSRNOG00000003670	2 retrocopies	retro_rnor_418, retro_rnor_67,
Rattus norvegicus	ENSRNOG00000038489	1 retrocopy	retro_rnor_2158,
Sarcophilus harrisii	ENSSHAG00000002220	20 retrocopies	retro_shar_152, retro_shar_201, retro_shar_232, retro_shar_259, retro_shar_308 , retro_shar_319, retro_shar_361, retro_shar_374, retro_shar_398, retro_shar_461, retro_shar_477, retro_shar_487, retro_shar_505, retro_shar_545, retro_shar_546, retro_shar_575, retro_shar_673, retro_shar_680, retro_shar_789, retro_shar_810,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Ictidomys tridecemlineatus	ENSSTOG00000010587	2 retrocopies	retro_itri_116, retro_itri_1259,
Ictidomys tridecemlineatus	ENSSTOG00000024685	10 retrocopies	retro_itri_1017, retro_itri_1123, retro_itri_1355, retro_itri_202, retro_itri_264, retro_itri_272, retro_itri_79, retro_itri_921, retro_itri_981, retro_itri_983,
Takifugu rubripes	ENSTRUG00000014892	1 retrocopy	retro_trub_25,