RetrogeneDB ID: retro_shar_205

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834650.1:678984..679418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSSHAG00000016835
• Aliases: None
• Description: succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa [Source:HGNC Symbol;Acc:10682]

Sequence

>retro_shar_205
GTCAGAAATGCTATTTCTGGGAAAAAAAACAGCTAAGGAAGAGATGGAACATTTCTGGAACAGGAACATCAATTCAAATC
ATCTGTTGTCACCTCATGTCACTATTTATAGCTAGTCCCTGCCTATGACAATGTCCATTAGTCACTGAGGTGCTAGTGTT
GCCTTGAGTGCAAGGCTATTCTTTTTTTGGATTGGCAGCCTTATTGATCCCTGAGAATTTCGAGATTCTCTTGGAGTTTG
TAAAATCTTGGGCCTAGGACCAGCTCTGATCTACCCGGCCAAGTTTTCTCTAGTCTTCTTTCTTATGTACCATACATCAA
ATGGAATCCAACACTTGACCTAGATCTAGGGAAGGCCTAAAGATTCCTGAGTTCTACCAGTCTGGAGAAATTGTCTTGGT
TCTCACTCTGTTTTCCTCTGTAGAACTAGCAGCC

Alignment

ORF - retro_shar_205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.33 %
• Parental protein coverage: 85.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VRNAIP-LGTAAKEEMEHFWNKNINSNRPLSPHITIYSWSLPMMMSITHRGTGVALSA-GVSLFGLAALL
          VRNAI......AKEEMEHFWN.NINSN..LSPH.TIYS.SLPM.MSI.H.G..VALSA.G.S.FGLAALL
Retrocopy VRNAIS>XXXXAKEEMEHFWNRNINSNHLLSPHVTIYS*SLPMTMSISH*GASVALSA>GYSFFGLAALL

Parental  LPGSFESHLQLVKA-LGLGSSLIYTAKFALVFPLMYHTWNGIRHLM-WDLGK-GLKIPQLYQSGVAVLVL
          .P..FE..L..VK..LGLG..LIY.AKF.LVF.LMYHT.NGI.HL...DLGK.GLKIP..YQSG..VLVL
Retrocopy IPENFEILLEFVKS<LGLGPALIYPAKFSLVFFLMYHTSNGIQHLT<LDLGK<GLKIPEFYQSGEIVLVL

Parental  TVLSSVGLAA
          T..SSV.LAA
Retrocopy TLFSSVELAA

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_205 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 18 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015351	2 retrocopies	retro_amel_468, retro_amel_803,
Bos taurus	ENSBTAG00000015853	1 retrocopy	retro_btau_835,
Canis familiaris	ENSCAFG00000012992	2 retrocopies	retro_cfam_1529, retro_cfam_275,
Callithrix jacchus	ENSCJAG00000004757	3 retrocopies	retro_cjac_1119, retro_cjac_2455, retro_cjac_988,
Echinops telfairi	ENSETEG00000015767	1 retrocopy	retro_etel_675,
Felis catus	ENSFCAG00000000499	1 retrocopy	retro_fcat_1609,
Homo sapiens	ENSG00000143252	4 retrocopies	retro_hsap_1794, retro_hsap_1896, retro_hsap_609, retro_hsap_854,
Gorilla gorilla	ENSGGOG00000008017	3 retrocopies	retro_ggor_1390, retro_ggor_536, retro_ggor_697,
Macaca mulatta	ENSMMUG00000012411	11 retrocopies	retro_mmul_1063, retro_mmul_1323, retro_mmul_1338, retro_mmul_1686, retro_mmul_1845, retro_mmul_2002, retro_mmul_2087, retro_mmul_239, retro_mmul_2416, retro_mmul_369, retro_mmul_672,
Mustela putorius furo	ENSMPUG00000014439	1 retrocopy	retro_mputfur_1201,
Nomascus leucogenys	ENSNLEG00000014367	3 retrocopies	retro_nleu_1476, retro_nleu_420, retro_nleu_439,
Pan troglodytes	ENSPTRG00000001585	4 retrocopies	retro_ptro_1274, retro_ptro_2458, retro_ptro_449, retro_ptro_593,
Pteropus vampyrus	ENSPVAG00000005544	2 retrocopies	retro_pvam_879, retro_pvam_974,
Rattus norvegicus	ENSRNOG00000003163	2 retrocopies	retro_rnor_1486, retro_rnor_1487,
Sarcophilus harrisii	ENSSHAG00000016835	1 retrocopy	retro_shar_205 ,
Sus scrofa	ENSSSCG00000030318	2 retrocopies	retro_sscr_1050, retro_sscr_1061,
Takifugu rubripes	ENSTRUG00000001873	1 retrocopy	retro_trub_41,
Tursiops truncatus	ENSTTRG00000009234	1 retrocopy	retro_ttru_196,