RetrogeneDB ID: retro_shar_668

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856979.1:1461368..1461876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000000409
• Aliases: None
• Description: None

Sequence

>retro_shar_668
ACTGCTCTTTATCTTGTTGCACCTAAGCAGAATAAACTGGACATGGTCGAAAAGGAGTTACTCAAGAGTAATAAAACTTT
TGAAGGAACCCAAGATGATTGTCTCTATTATGAATCTTCATATAAAGCTTTCTATTAAGATCAAAATCCTAAGTAACATT
GTAGCAAAAGTGAAATTCCCCCCATCTCAACCAACATCACAAAGTTGCTTCTTGAAAATGATTGCTTAAACAATATTCCA
GGAGTCATTTCAACATTTTCTGCCATGGGGGTGTGTGCATCATGGAGAAGTACAGTACTCAGTTACTACTGTTCTAATTT
AGCTATCTCTTTCAGAATTAAAAACAGTCCTGAACAGCTTTCTAAGTAAAAGCAACATCTTAAAAATGGAGGTCTACATT
GACCCTTAAATCATCAGAGGAATGATTATTGGTATAGGAGATAAATGTTTTGATATGTTTGTAAAAATCAAGATCTAGAA
GCTAAGCGGGATAATGAAAGAAGCTATT

Alignment

ORF - retro_shar_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.79 %
• Parental protein coverage: 80.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TALFSAASKQNKLDVVEKELL-RVTKLLKDPKMVDSIMNPHIKRSIKIKTLSDIIAKERFSP-ITTNLMK
          TAL...A.KQNKLD.VEKELL.RV.KLLK.PKM..SIMN.HIK.SIKIK.LS.I.AK..F.P.I.TN..K
Retrocopy TALYLVAPKQNKLDMVEKELL>RVIKLLKEPKMIVSIMNLHIKLSIKIKILSNIVAKVKFPP<ISTNITK

Parental  LLAENGRLNNTEGVISAFSTMM-SVHRGEVQCLVTTASTLDSATLSELKAVLNGFLSKGQVLKMEVKTDP
          LL.EN..LNN..GVIS.FS.M...VH.GEVQ..VTT...L....LSELK.VLN.FLSK...LKMEV..DP
Retrocopy LLLENDCLNNIPGVISTFSAMG>CVHHGEVQYSVTTV--LI*LSLSELKTVLNSFLSKSNILKMEVYIDP

Parental  SIMGGMIVRIGEKYVDMSAKTKIQKLSRIMREAI
          .I..GMI..IG.K..DM..K.KI.KLS.IM.EAI
Retrocopy *IIRGMIIGIGDKCFDMFVKIKI*KLSGIMKEAI

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_668 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.

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014708	1 retrocopy	retro_amel_1914,
Canis familiaris	ENSCAFG00000009541	3 retrocopies	retro_cfam_1277, retro_cfam_2198, retro_cfam_235,
Choloepus hoffmanni	ENSCHOG00000011242	1 retrocopy	retro_chof_638,
Callithrix jacchus	ENSCJAG00000002873	1 retrocopy	retro_cjac_1567,
Equus caballus	ENSECAG00000009059	1 retrocopy	retro_ecab_633,
Echinops telfairi	ENSETEG00000000807	5 retrocopies	retro_etel_1412, retro_etel_1906, retro_etel_507, retro_etel_839, retro_etel_841,
Felis catus	ENSFCAG00000028656	1 retrocopy	retro_fcat_1511,
Homo sapiens	ENSG00000241837	1 retrocopy	retro_hsap_2377,
Gorilla gorilla	ENSGGOG00000012611	1 retrocopy	retro_ggor_1803,
Macropus eugenii	ENSMEUG00000006613	4 retrocopies	retro_meug_122, retro_meug_1552, retro_meug_381, retro_meug_805,
Myotis lucifugus	ENSMLUG00000008224	3 retrocopies	retro_mluc_1833, retro_mluc_826, retro_mluc_856,
Macaca mulatta	ENSMMUG00000015504	1 retrocopy	retro_mmul_253,
Monodelphis domestica	ENSMODG00000021057	2 retrocopies	retro_mdom_280, retro_mdom_95,
Mustela putorius furo	ENSMPUG00000001319	5 retrocopies	retro_mputfur_1593, retro_mputfur_1628, retro_mputfur_1639, retro_mputfur_581, retro_mputfur_918,
Mus musculus	ENSMUSG00000022956	2 retrocopies	retro_mmus_2196, retro_mmus_955,
Otolemur garnettii	ENSOGAG00000015850	4 retrocopies	retro_ogar_3518, retro_ogar_418, retro_ogar_559, retro_ogar_944,
Pongo abelii	ENSPPYG00000011384	1 retrocopy	retro_pabe_2247,
Pan troglodytes	ENSPTRG00000013876	1 retrocopy	retro_ptro_1739,
Rattus norvegicus	ENSRNOG00000001991	1 retrocopy	retro_rnor_2210,
Sarcophilus harrisii	ENSSHAG00000000409	3 retrocopies	retro_shar_369, retro_shar_389, retro_shar_668 ,
Sus scrofa	ENSSSCG00000012042	2 retrocopies	retro_sscr_226, retro_sscr_566,
Ictidomys tridecemlineatus	ENSSTOG00000008658	3 retrocopies	retro_itri_1030, retro_itri_565, retro_itri_794,