RetrogeneDB ID: retro_shar_258

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835536.1:30837..31592(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000002384
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEPT7
• Ensembl ID: ENSSHAG00000003788
• Aliases: None
• Description: septin 7 [Source:HGNC Symbol;Acc:1717]

Sequence

>retro_shar_258
GACTCCATCGACAGCAAGTTCGAGGACTACCTGAACGCCGAGTCGCGGGTCTACCGGCGGCAGACGCCCGACAGCCGGGT
GCAGGGCTGCCTGTACTTCCTCTCCCCGTCGGGCCGCGGCCTCAAGCCGCTGGACGCGGAGTTCATGAAGCGCCTGCACG
ACAAGGTCAACGTCATCCTCCTCATTGCCAAAGCCGACACGCTGACGCCCGAGGAGTGCCGGCGCTTCAAGAAGCGCATC
ATGAGGGAGATCCAGGAGCACCAGATTAAGATCTACGAGTTCCCGGGCCCGGGCGACGCCGCGGGCCAGAAGCCGGTCCG
GAAGATCCGCGACCGCCTGCCGCTCGCCGTGGTGGCCAGCGACACCGTGGTGCAGGTGGACGGCCGGAGGGTGCGGGGCA
GGAAGTACCCCTGGGGCGTGGCCGAGGTGGAGAACGGCGATCACTGCGACGTCGCCATCCTCCGCCACATGCTGATGCGC
ACCCACACCCAGCACCTGAGGGACGTCACCAACAACGTGCACTACGAGAACTACCGCAGCCCGAAGCTGCCCGGAGCCGG
GCCCAGCCGCTCCCCAGCCCGCGGGCGCAGAGGGAGGAGCACGCGGCCCGCCTGCGGGAGCTGGAGGCGCGCATGCAGCG
CGTGTGCGAGCTCAAGCTGCGGGAGAAGGTGCAGAGGCTGCGGGAGTCCGAGGCGCAGCTGCTGCAGCGCCGCGAGCAGA
TGAGGCTCGCCCTGGAGCAACAGCACCGGGAGCTG

Alignment

ORF - retro_shar_258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.16 %
• Parental protein coverage: 59.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DYIDSKFEDYLNAESRVNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHDKVNVIPLIAKADTLTP
          D.IDSKFEDYLNAESRV.RRQ.PD.RVQ.CLYF..PSG.GLKPLD.EFMKRLHDKVNVI.LIAKADTLTP
Retrocopy DSIDSKFEDYLNAESRVYRRQTPDSRVQGCLYFLSPSGRGLKPLDAEFMKRLHDKVNVILLIAKADTLTP

Parental  EECQQFKKQIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGV
          EEC..FKK.IM.EIQEH.IKIYEFP...D....K.V.KI.DRLPLAVV.S.T...V.G.RVRGR.YPWGV
Retrocopy EECRRFKKRIMREIQEHQIKIYEFPGPGDAAGQKPVRKIRDRLPLAVVASDTVVQVDGRRVRGRKYPWGV

Parental  AEVENGDHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNKGQLTK-SPLAQME
          AEVENGDHCD..ILR.ML.RTH.Q.L.DVTNNVHYENYRS.KL..............G..T....L...E
Retrocopy AEVENGDHCDVAILRHMLMRTHTQHLRDVTNNVHYENYRSPKLPGAGPSRSPARGRRGRSTR<ARLRELE

Parental  EERREHVAKMKKMEMEMEQVFEMKVKEKVQKLKDSEAELQRRHEQM
          ..R...V...K..E.......E.......Q........L...H...
Retrocopy -ARMQRVCELKLRE-KVQRLRESEA-QLLQRREQMRLALEQQHREL

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_258 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Equus caballus	ENSECAG00000022693	1 retrocopy	retro_ecab_650,
Echinops telfairi	ENSETEG00000015624	3 retrocopies	retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens	ENSG00000122545	2 retrocopies	retro_hsap_3810, retro_hsap_4202,
Gorilla gorilla	ENSGGOG00000001175	1 retrocopy	retro_ggor_2816,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Nomascus leucogenys	ENSNLEG00000001673	1 retrocopy	retro_nleu_2152,
Otolemur garnettii	ENSOGAG00000006015	1 retrocopy	retro_ogar_1193,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853,
Rattus norvegicus	ENSRNOG00000006545	9 retrocopies	retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428, retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258 ,
Sarcophilus harrisii	ENSSHAG00000007189	1 retrocopy	retro_shar_59,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736, retro_itri_1771,
Tursiops truncatus	ENSTTRG00000016197	1 retrocopy	retro_ttru_329,