RetrogeneDB ID: retro_meug_175

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_5120:59818..60337(+)
• Located in intron of: ENSMEUG00000015449

Retrocopy information

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

Parental gene information

• Parental gene symbol: TYMS
• Ensembl ID: ENSMEUG00000009507
• Aliases: None
• Description: thymidylate synthetase [Source:HGNC Symbol;Acc:12441]

Sequence

>retro_meug_175
TATGGTTTCCAGTGGAGACATTGTGGGGCAGAATACAAAGAGATGAACACAGATTATTCTGGGCAAGGAGTCATTGAGGC
AACCAAAACCAACCCTGATGACAGAAGGATCATTATGTGTACTTGGAATCCTAAAGATCTTCCTCTGATGGCACTGCCTC
CATACCATGCTCTCTACCAGTTCTATGTATTGAATGGTGAGCTTTTTTGTCAACTATACCAGTGATGTGGAGACATGGGC
CTCCAGGTGTCATTCAACATTGCCAGTTATTCCCTGCTCACCTACATGATTGCTCACATCCCAGGCCTAAAGTCAGGTGA
TTTTGTACACATTCTGGGAGATGCTCACATATACTTGAATCATATTGGGCCACTGAAAATTCAGATTCAGCAAGAACCAA
GACCTTTCCCAAAGCTCAAAATTCTTCAAAAAGTTGAAACCACTGATGATTTCAAGGCTAAGGATTTCCTGATTAAAGAC
TACAATGCTCACCCAGCTATTAAAATGGAGATGGCCATC

Alignment

ORF - retro_meug_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.57 %
• Parental protein coverage: 53.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGAEYKEMNTDYSGQGVDQL-QKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVLNGELSC
          .G.........Y.....D...Q.VI...KTNPDDRRIIMC.WNPKDLPLMALPP.HAL.QFYVLNGEL.C
Retrocopy YGFQWRHCGAEYKEMNTDYSGQGVIEATKTNPDDRRIIMCTWNPKDLPLMALPPYHALYQFYVLNGELFC

Parental  QLYQRSGDMGLGVPFNIASYALLTYMIAHVTGLKPGDFVHTLGDAHIYLNHIEPLKIQIQREPRPFPKLK
          QLYQ..GDMGL.V.FNIASY.LLTYMIAH..GLK.GDFVH.LGDAHIYLNHI.PLKIQIQ.EPRPFPKLK
Retrocopy QLYQ*CGDMGLQVSFNIASYSLLTYMIAHIPGLKSGDFVHILGDAHIYLNHIGPLKIQIQQEPRPFPKLK

Parental  ILRRVETIDDFKAEDFLIEDYNPHPAIKMEMAV
          IL..VET.DDFKA.DFLI.DYN.HPAIKMEMA.
Retrocopy ILQKVETTDDFKAKDFLIKDYNAHPAIKMEMAI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_175 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_175 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,