RetrogeneDB ID: retro_shar_424

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842086.1:43064..43665(+)
• Located in intron of: ENSSHAG00000000524

Retrocopy information

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

Parental gene information

• Parental gene symbol: TYMS
• Ensembl ID: ENSSHAG00000003102
• Aliases: None
• Description: thymidylate synthetase [Source:HGNC Symbol;Acc:12441]

Sequence

>retro_shar_424
GACTTTTTGGACAAGCAGGGATTCACTACCAGGGAGGAAGGAGATTTGGGGCCAGTGTATGGCTTCCAGTAGAGACATTT
TGGGTCAGAATATAAAGAAATGAACACAGATTATTCCAGGCAAAGAATAGATCAACTACAAAAATTAATTGACACAATCA
AAACCAACCCTGATGAAAGAAGGATCATGTGTGCTTAGAATTCTAAATCCTAAAGGAATCTTCCTCTGATGGCACTTCCT
CTGTGTCACACTCTCTGTTAGTTCTTTGTATTAAATGGCAAGCTCTCTTGTTAGTTATATCAAAGATCTGGAGATGAGGG
TCTCAGGATGCTGTTCAACATTGCCAGTTATTCCCTGCTCACCTACATGATGGCCCAAGTCAAAGGCCTAAAGCCAGGTG
AATTTGTACATAATTCTGGGAGATACTCATATATACCTGAATCGTATTAAGCTACTGAAAATTCAGTTTCAGCAAGAACC
AAGACCTTTCCCTAAGCTCAAAATTCTTTGAAAAGTTGAAACTATTGATGATTTCAAGGCCGAGGACTTCCTTATTGAAG
ACTACAATCCTCATCCAGCTATTAAAATGGAGATGGCTGTC

Alignment

ORF - retro_shar_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.19 %
• Parental protein coverage: 80.82 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFLDKQGFTTREEGDLGPVYGFQWRHFGAEYKEMNTDYSGQGIDQLQKVIDTIKTNPDDRRIIMCAWNPK
          DFLDKQGFTTREEGDLGPVYGFQ.RHFG.EYKEMNTDYS.Q.IDQLQK.IDTIKTNPD.RR.IMCA.N.K
Retrocopy DFLDKQGFTTREEGDLGPVYGFQ*RHFGSEYKEMNTDYSRQRIDQLQKLIDTIKTNPDERR-IMCA*NSK

Parental  ---DLPLMALPPCHALCQFYILNGELSCQLYQRSGDMGLGVPFNIASYSLLTYMIAHVTGLKPGDFVHT-
          ....LPLMALP.CH.LC.F..LNG.LSC.LYQRSGD.GL...FNIASYSLLTYM.A.V.GLKPG.FVH..
Retrocopy S*RNLPLMALPLCHTLC*FFVLNGKLSC*LYQRSGDEGLRMLFNIASYSLLTYMMAQVKGLKPGEFVHN>

Parental  LGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKVEAIDDFKAEDFLIEDYNPHPAIKMEMAV
          LGD.HIYLN.I..LKIQ.Q.EPRPFPKLKIL.KVE.IDDFKAEDFLIEDYNPHPAIKMEMAV
Retrocopy LGDTHIYLNRIKLLKIQFQQEPRPFPKLKIL*KVETIDDFKAEDFLIEDYNPHPAIKMEMAV

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_424 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009230	2 retrocopies	retro_fcat_1107, retro_fcat_339,
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084, retro_mdom_1186,
Mustela putorius furo	ENSMPUG00000005419	2 retrocopies	retro_mputfur_1155, retro_mputfur_860,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956, retro_ogar_3211,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424 ,
Sus scrofa	ENSSSCG00000023869	2 retrocopies	retro_sscr_810, retro_sscr_841,