RetrogeneDB ID: retro_shar_427

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842236.1:97815..98633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRBF2
• Ensembl ID: ENSSHAG00000004744
• Aliases: None
• Description: nuclear receptor binding factor 2 [Source:HGNC Symbol;Acc:19692]

Sequence

>retro_shar_427
CTCAACCTGGCTCATCAGCAGAGCAGAAAAGCAGGCCGGTCACTAGCTGCAGGGAAATACAAAGAGGTCATTTTGTGTCA
CCAGAAGGCAGCTGCGAATCTTACTGAAGTCATGAAGCTGACACAGTCTGGACAGGCTCAGTTATCACTGGAATCACAAA
AGGATAGCCACGTGAAACACCTCTTGCTTATTCAGGAGAGGTGGAAAAGGGCAAAGAGGGAGGAAAGGTGGAGAGCCCAG
CAGACTCCCGATGGAGCCGCTTGGCTTCTGACGTCGTGCAAGATGGCCGAGGATGGGTCCGAGGGTCACAGTGCGCCTAG
ACCTCAGAAGTTTAGTCTCACTGCAGTGCCTGGGGTCTTGGATAGGGACCCAGACACTCTACTTTTTCTCCTTCAAAGAG
GAAAGACCTGACAGAACCGTGTCCTGGCAGCAAAGTCCCGAAATATGACAAGACCACGATAGAATAAGAGGCAAGCAAGA
TCTCTGATCTGAAGGGACATGTAGAGTTTCTCATTAACGACAAGGAAAGGTTGGGAAGAGAAAACAAGCAGCTCCGTGCT
GAAAAGGCCAGGCTCCAGAAGGCTCCCCTCGAAAAGGAATTGGATATAGATGCTGACTTTGTGGAAAAATCTGAATTAGG
GAGCCTGCCTTCCCCTTCAGAGACTGCTTTAGCCTCTTCTACCTGGCAGGAGTTTGCAGCAAACACAGGGAAAGCCAAGG
ACATTCCCATCCCCAACCTTCCCCGCTTGGACTTTCCATCCCCAGAGCTCCCATTTCTAGAACTCCCTGAAGATATTCTG
AAAGGACATATGAATAGT

Alignment

ORF - retro_shar_427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.31 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INRAHQQSRKADRSLAAGKYEEAILCHQKAAAYLTEAMKLTQSEQALLSLELQRDSHMKQLLLIQERWKR
          .N.AHQQSRKA.RSLAAGKY.E.ILCHQKAAA.LTE.MKLTQS.QA.LSLE.Q.DSH.K.LLLIQERWKR
Retrocopy LNLAHQQSRKAGRSLAAGKYKEVILCHQKAAANLTEVMKLTQSGQAQLSLESQKDSHVKHLLLIQERWKR

Parental  AKREERWRAQQTPDGTPQLLTSCKMAEDGSECHSVPRSQQFSPAVVPGVLDRDPDTLLFLLQ-KRKDPTE
          AKREERWRAQQTPDG...LLTSCKMAEDGSE.HS.PR.Q.FS...VPGVLDRDPDTLLFLLQ.KRKD.TE
Retrocopy AKREERWRAQQTPDGAAWLLTSCKMAEDGSEGHSAPRPQKFSLTAVPGVLDRDPDTLLFLLQ<KRKDLTE

Parental  PSPGSKVPKDDKTTIEEQATKIADLKRHVEFLVADNERLRRENKQLRAEKARLQKAPLEKELDVDADFVE
          P.PGSKVPK.DKTTIE..A.KI.DLK.HVEFL..D.ERL.RENKQLRAEKARLQKAPLEKELD.DADFVE
Retrocopy PCPGSKVPKYDKTTIE*EASKISDLKGHVEFLINDKERLGRENKQLRAEKARLQKAPLEKELDIDADFVE

Parental  KSELWSLPPPSETASASSTWQEFAANTGKAKDIPIPNLPPLDFPSPELPLLELPEDILKGLMNS
          KSEL.SLP.PSETA.ASSTWQEFAANTGKAKDIPIPNLP.LDFPSPELP.LELPEDILKG.MNS
Retrocopy KSELGSLPSPSETALASSTWQEFAANTGKAKDIPIPNLPRLDFPSPELPFLELPEDILKGHMNS

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_427 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427 ,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183,