RetrogeneDB ID: retro_mputfur_1155

Retrocopy location

• Organism: Ferret (Mustela putorius furo)
• Coordinates: GL897028.1:3238483..3239379(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TYMS
• Ensembl ID: ENSMPUG00000005419
• Aliases: None
• Description: thymidylate synthetase [Source:HGNC Symbol;Acc:12441]

Sequence

>retro_mputfur_1155
TCCCCACCCGCCACATAGAGGTGTGGTATGGAGCCCTTGGCCTCCACCCCATGGGAAGCTGCAGTACCTGGGGCAGATCC
AGCACATCCTTCACTGAAGGTTCCAGAAGGATGAGAGCACTGGCACCAGCATGCTGGGGTGTTTGGCATGCAGTTGCACT
ACAGCCTGAGAGATGAATTTCCTTTGCTGATAACAACACATATATTCTGAAAGAGTGTTTTGGAGGAGTTACAGTGTTTT
ATCAAGGGCTTTACAAATGCTAAGGAACTGTCTCCTAAGGGAGTGAAAATCTGGGAAGTCAATGCCTCCTAAGACTTCTT
GGACAACCTGGGATTTTCCAATAGAGAAAAGGGGATTTAGGTTCAATTTATGGTTCTCAGTGGAGAAGGCATTTTGGGGC
AGAATACAAAGATGAGGATTCAGATTATTCAAGTTAAGGAGTACACTAACTGCAAAAGATGCTTCGCACAGTTGAAATCA
AACTCAAGGACAGAAGAATTATCTTGTGTGGTTGGAATCCCAAAGCACTTCCTTTTATGGCCCTATCTCCCTGCCATACC
TTTCCCAGATCTCCATGGTGAGCGGTGAGCTGTCCTGCCAGCTGTACTGGAGGGAAGGAGACATGGTTTTGGCTGTGTCC
TTCAACTTGGCCCTCCACACCTGGCCCACTATATGATCACACACATCAAAGGCCTGAAAGCAGGTGACTTCATACATATT
TTGAAGATACACATATTTGCCTGAATTATGTTGAACCTCTAAAAGTGCAGCTTCAGTGAGAACCAGCACCTTTCCTAAAG
CTCAAAATCCTTCAAAAAGGTGAGACCATCCATGACTTCAAGGCTGAAGACTTTCTTCACAGTATTCACCCAACTATTAA
AATGAAAATGGATATC

Alignment

ORF - retro_mputfur_1155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.72 %
• Parental protein coverage: 94.97 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SPPAAQKPAAEPQ-PAPHGELQYLGQIEHILRCGVRKDDRTGTGTLS-VFGMQARYSLRDEFPLLTTKRV
          SPPA......EP..P.PHG.LQYLGQI.HIL.....KD..TGT..L..VFGMQ..YSLRDEFPLL.T...
Retrocopy SPPAT*RCGMEPL>PPPHGKLQYLGQIQHILH*RFQKDESTGTSMLG<VFGMQLHYSLRDEFPLLITTHI

Parental  FWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSNRE-EGDLGPVYGFQW-RHFGAEYI
          F.K.VLEEL..FIKG.TNAKELS.KGVKIW..N.S.DFLD.LGFSNRE..GDLG..YG.QW.RHFGAEY.
Retrocopy F*KSVLEELQCFIKGFTNAKELSPKGVKIWEVNAS*DFLDNLGFSNRE<KGDLGSIYGSQWRRHFGAEYK

Parental  DKDSDYSGQGVDQLQKVIDTIKTNPDDRRIILCGWNPKDLPLMALPPCHA-LCQFYVVNGELSCQLYQRS
          D.DSDYS..GV..LQK...T......DRRIILCGWNPK.LP.MAL.PCH..L.Q...V.GELSCQLY.R.
Retrocopy DEDSDYSS*GVH*LQKMLRTVEIKLKDRRIILCGWNPKALPFMALSPCHT<LSQISMVSGELSCQLYWRE

Parental  GDMGLGVPFNIASYA-LLTYMIAHITGLKPGDFVHTL-GDAHIYLNHIEPLKMQLQREPRPFPKLKILRK
          GDM.L.V.FN.A....L..YMI.HI.GLK.GDF.H.L..D.HI.LN..EPLK.QLQ.EP.PF.KLKIL.K
Retrocopy GDMVLAVSFNLALHT<LAHYMITHIKGLKAGDFIHIL<EDTHICLNYVEPLKVQLQ*EPAPFLKLKILQK

Parental  VETIDDFKAEDFQIEGYSPHPTIKMEMAV
          .ETI.DFKAEDF.....S.HPTIKM.M..
Retrocopy GETIHDFKAEDFL---HSIHPTIKMKMDI

Legend:

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

Expression

RNA-Seq

Mustela putorius furo was not studied using RNA-Seq expression data.

ChIP-Seq

Mustela putorius furo was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mputfur_1155 retrocopy.

TSS

Mustela putorius furo was not studied using FANTOM5 data.

Lab

retro_mputfur_1155 was not experimentally validated.

Homology

Retrocopy orthology:

Mustela putorius furo 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 8 parental genes, and 13 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,