RetrogeneDB ID: retro_tsyr_1130

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_31645:1772..2283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSTSYG00000013759
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_tsyr_1130
CAGCATAGGTGCTTATTTATTCAGACACCTAAGATTGTGACAGATAAAGATTACTCGGGACCGCCAGTTCTAAGATTGTG
GTGGTAACTGCAGGAGTCCGTCAGCAAGAGGGGGAAGCCGTTTCAATCTGGTACAGAGAAATGTTAATGTCTCCAAATTC
ATTATTCCTCAGATTGTCAAGTGCAGTCCTGATGGCCTCATAATTGTGGTTTCCAACCCAGTGGACATTCTTACATATGT
TACCTGGAAACTAAGTGGATTACCCAAGCATCGTGTGATTAGAAGTGGGGGTACTCTGGATTCTGCTAGATTTTGCTACC
TTTTGGCTGAAAAACTTGGCATTCATTCCAGCTGCTGCCATGGATAGGTTTTGAGAGAACATGGCGACTCAAGTGTGGCT
GTGCTGAGTGGAGTGAACATGGCAGGTATTTCTTTTCAGGCATCGAATCCAGAAATGGGAACTGACAATGACAGTGAAAA
TTGGAAGGAAGTGCATAAGATGGTGGGTGAA

Alignment

ORF - retro_tsyr_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 58.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QHGSLFLQTPKIVADKDYSV-TANSKIVVVTAGVRQQEGE-SRLNLVQRNVNVFKFIIPQIVKYSPDCII
          QH..LF.QTPKIV.DKDYS..TA.SKIVVVTAGVRQQEGE.SR.NLVQRNVNV.KFIIPQIVK.SPD..I
Retrocopy QHRCLFIQTPKIVTDKDYSG<TASSKIVVVTAGVRQQEGE<SRFNLVQRNVNVSKFIIPQIVKCSPDGLI

Parental  IVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLSIHPSSCHGWILGEHGDSSVAVWSG
          IVVSNPVDILTYVTWKLSGLPKHRVI.SG..LDSARF.YL.AEKL.IH.S.CHG..L.EHGDSSVAV.SG
Retrocopy IVVSNPVDILTYVTWKLSGLPKHRVIRSGGTLDSARFCYLLAEKLGIHSSCCHG*VLREHGDSSVAVLSG

Parental  VNVAGVSLQELNPEMGTENDSENWKEVHKMVVE
          VN.AG.S.Q..NPEMGT.NDSENWKEVHKMV.E
Retrocopy VNMAGISFQASNPEMGTDNDSENWKEVHKMVGE

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1130 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 15 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Homo sapiens	ENSG00000111716	1 retrocopy	retro_hsap_4863,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Pongo abelii	ENSPPYG00000004356	3 retrocopies	retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
Pan troglodytes	ENSPTRG00000004762	1 retrocopy	retro_ptro_3237,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,
Tarsius syrichta	ENSTSYG00000013759	7 retrocopies	retro_tsyr_1130 , retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,