RetrogeneDB ID: retro_shar_331

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841366.1:2185706..2186507(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPN
• Ensembl ID: ENSSHAG00000002111
• Aliases: None
• Description: centromere protein N [Source:HGNC Symbol;Acc:30873]

Sequence

>retro_shar_331
AAAGATATCTCCCAGCAAATGGTTGAACTTTGTAAGAAGAAACATGAAAAAATGAAAGCTGCAATTTTAGACATAATTTA
TCATCAAACTTGCTAAATCAAGAAAATTTGCATTGTTTATAAAATGACTAAACTCCCTGGTGAAGAGGTTGACCTTTCTG
ATATAGAAAAATTTAAAGATACTTTAAAGAAAATTCTTCAGAGAGCCTTAAGAAATGTACATACCAGCTTCAGAGATAGT
AAGGATAATAATGTAATATGGATTTGAATTGCCTGGGGAACATCTTACATGAAACCAGACCAGTACAAAATAACTTATGT
GATATATCATTCTTAAATTCTTTTCGTCTTCATCTCTTCCTGCCGTGTTAAGAAGTACATTCCAGAGCTCTGATACGCAC
TCATGACTACTGGCAATCAACATAAGATCCAACAAGTGGAGCTCCAAAGTCTATATCTGGATTCTCTTAAGGCTATTGTT
TTTAAACAGTAAAGTCCGGATTTTCAAGCTTAGTATCTTACACCTTTGCAGGAAGGAAATACTGAAATAAAATAGTGGAC
CCAAGGATCATTCATGAAAATATAAAAGAAAAGGAAAGAATCCAAAAGAATGACATGGAAAATTTGGGGGGATTATATTC
AACCCAGAATAGAATTTGCACAGTATAAGCTTAAAACCAAATTCAAAATTGACTCTAAAAATGGCATTTTGATTGAAAGG
GAAGAACTTTTCACATACTTGGTTAAATTCTCTAGTCTACATCTTTTGGAAGCATTGAAATCTTTAGCACCAGATGGTAT
T

Alignment

ORF - retro_shar_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 79.35 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDVCQQVVELCKKKRASMEEAAILDIIYHQTCQIKKIWIVYKMTKTPDEEVDLFDMEEFKDTFKKVLQRA
          .D..QQ.VELCKKK...M..AAILDIIYHQTC.IKKI.IVYKMTK.P.EEVDL.D.E.FKDT.KK.LQRA
Retrocopy KDISQQMVELCKKKHEKMK-AAILDIIYHQTC*IKKICIVYKMTKLPGEEVDLSDIEKFKDTLKKILQRA

Parental  LKNVHISFRDYEDN-AVWIRIAWGTPYMQPNQYKTTYVVYYSQTPFVFISHCRVKKYIPELWQALMTAGN
          L.NVH.SFRD..DN...WI.IAWGT.YM.P.QYK.TYV.Y.S...FVFIS.CRVKKYIPEL..ALMT.GN
Retrocopy LRNVHTSFRDSKDNNVIWI*IAWGTSYMKPDQYKITYVIYHS*ILFVFISSCRVKKYIPEL*YALMTTGN

Parental  YHKIRQMELRSLYLDSLKSIVFKQYNQDFQTYCLTPLQEGNTE-NEIATVDPRIINENVKEKERIQ-RVT
          .HKI.Q.EL.SLYLDSLK.IVFKQ...DFQ...LTPLQEGNTE.N.I..VDPRII.EN.KEKERIQ.R.T
Retrocopy QHKIQQVELQSLYLDSLKAIVFKQ*SPDFQA*YLTPLQEGNTE<NKI--VDPRIIHENIKEKERIQ>RMT

Parental  RETFGDYVQPRIEFAQYKLETKFKIDSKNGILAEREEPFRCLVKFSSPHLLEALKSLAPAGI
          ....GDY.QPRIEFAQYKL.TKFKIDSKNGIL.EREE.F..LVKFSS.HLLEALKSLAP.GI
Retrocopy WKIWGDYIQPRIEFAQYKLKTKFKIDSKNGILIEREELFTYLVKFSSLHLLEALKSLAPDGI

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_331 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011635	1 retrocopy	retro_btau_1101,
Felis catus	ENSFCAG00000004978	1 retrocopy	retro_fcat_1852,
Homo sapiens	ENSG00000166451	2 retrocopies	retro_hsap_2146, retro_hsap_2291,
Oryctolagus cuniculus	ENSOCUG00000000024	3 retrocopies	retro_ocun_1676, retro_ocun_1806, retro_ocun_528,
Sarcophilus harrisii	ENSSHAG00000002111	1 retrocopy	retro_shar_331 ,
Ictidomys tridecemlineatus	ENSSTOG00000007345	1 retrocopy	retro_itri_1431,
Tupaia belangeri	ENSTBEG00000000039	2 retrocopies	retro_tbel_2049, retro_tbel_3055,