RetrogeneDB ID: retro_tsyr_1465

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_45104:4728..5201(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLA1
• Ensembl ID: ENSTSYG00000012350
• Aliases: None
• Description: lysophospholipase I [Source:HGNC Symbol;Acc:6737]

Sequence

>retro_tsyr_1465
TTTGATATTGTTGGACTTTCACCCTATTCACAGGAGGATGAAGCTGGAATTAAACAGGCAGCAGAAAATATAAAAGCTCT
GATCAATCAAGTGGTGAAGAATGGCATTCCTTCTAATGGAAATATTTTGGAAGGATTTTCTCAGGAAGGAGCTTTATCTT
TATATACTGCTCTCACCACGCAGCAGAAACTGGCAGGTGTTACTGCACTAAGTTGCTGGCTTCCTCTTTGGGGCTTTGTT
TCCAAAGGGTCATATCAGTGGCACTAATAAAGATATTTCTATACGCCAATGCCATGGAAATTGTGACCCTCTAGTTCCCC
TGATGTTTAGTTCTCTTACTGTTGAAAAACTAAAAACATTGGTTGATCCAGCCATGTAACCTTTAAAACCTATGGAGGAA
TGATGCACAGTTCATGTCAACGGAAATGATGGATATCAAGCAATTCACTGATTAACTCCTACCTCCAATTGAT

Alignment

ORF - retro_tsyr_1465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.23 %
• Parental protein coverage: 80.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FDIVGLSPDSQEDEAGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTAL
          FDIVGLSP.SQEDEAGIKQAAENIKALI.Q.VKNGIPSN..IL.GFSQ.GALSLYTALTTQQKLAGVTAL
Retrocopy FDIVGLSPYSQEDEAGIKQAAENIKALINQVVKNGIPSNGNILEGFSQEGALSLYTALTTQQKLAGVTAL

Parental  SCWLPL-RTSFPKGPISGTNKDIPILQCHGDCDPLVPLLFGSLTAEKLKTLVDPA-NVTFKTYEGMMHSS
          SCWLPL....FPKG.ISGTNKDI.I.QCHG.CDPLVPL.F.SLT.EKLKTLVDPA..VTFKTY.GMMHSS
Retrocopy SCWLPL>GALFPKGHISGTNKDISIRQCHGNCDPLVPLMFSSLTVEKLKTLVDPA<HVTFKTYGGMMHSS

Parental  C-XXEMVDIKQFIDQLLPPID
          C...EM.DIKQF.D.LLPPID
Retrocopy C<STEMMDIKQFTD*LLPPID

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_1465 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 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006978	1 retrocopy	retro_cfam_523,
Callithrix jacchus	ENSCJAG00000011562	2 retrocopies	retro_cjac_1260, retro_cjac_3100,
Cavia porcellus	ENSCPOG00000022715	3 retrocopies	retro_cpor_142, retro_cpor_549, retro_cpor_782,
Dipodomys ordii	ENSDORG00000001479	1 retrocopy	retro_dord_88,
Equus caballus	ENSECAG00000016530	1 retrocopy	retro_ecab_238,
Echinops telfairi	ENSETEG00000001727	2 retrocopies	retro_etel_612, retro_etel_791,
Homo sapiens	ENSG00000120992	3 retrocopies	retro_hsap_3078, retro_hsap_3485, retro_hsap_3897,
Myotis lucifugus	ENSMLUG00000008208	1 retrocopy	retro_mluc_1683,
Macaca mulatta	ENSMMUG00000013157	3 retrocopies	retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Nomascus leucogenys	ENSNLEG00000001027	4 retrocopies	retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus	ENSOCUG00000006751	3 retrocopies	retro_ocun_1510, retro_ocun_1623, retro_ocun_1679,
Pongo abelii	ENSPPYG00000018590	3 retrocopies	retro_pabe_2550, retro_pabe_3177, retro_pabe_3565,
Pteropus vampyrus	ENSPVAG00000005246	2 retrocopies	retro_pvam_224, retro_pvam_838,
Rattus norvegicus	ENSRNOG00000008320	3 retrocopies	retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tarsius syrichta	ENSTSYG00000012350	6 retrocopies	retro_tsyr_1287, retro_tsyr_1303, retro_tsyr_1465 , retro_tsyr_1901, retro_tsyr_1996, retro_tsyr_2158,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,