RetrogeneDB ID: retro_tsyr_340

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_100081:6847..7087(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSTSYG00000012759
• Aliases: None
• Description: LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17017]

Sequence

>retro_tsyr_340
ATGCGTCTTCGGAAGCAAACCCCTAGTGACTTCTTAAAGCAAATCACCCGGCCGCCAGTTGTGGTAAAATTAAATTCTGG
AGTGGATTATCGAGGGGTCCTGGCTTGCCTGGGTGGCTACATGAATATCGCCCTGGAGCAGACAGAAGAATATGTGAATG
GCCAGCTGAAGGATAAGTACGGGGATGCATTTATCAGAGGAAACAATGTGTTGTACATCAGCACACAGAAGAGAAGGATG

Alignment

ORF - retro_tsyr_340 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSDF-KQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNV
          M.LRKQTPSDF.KQI...PVVVKLNSGVDYRGVLACL.GYMNIALEQTEEYVNGQLK.KYGDAFIRGNNV
Retrocopy MRLRKQTPSDFLKQITRPPVVVKLNSGVDYRGVLACLGGYMNIALEQTEEYVNGQLKDKYGDAFIRGNNV

Parental  LYISTQKRRM
          LYISTQKRRM
Retrocopy LYISTQKRRM

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_340 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 18 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Callithrix jacchus	ENSCJAG00000002482	4 retrocopies	retro_cjac_1173, retro_cjac_1278, retro_cjac_3176, retro_cjac_3248,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638,
Microcebus murinus	ENSMICG00000000571	1 retrocopy	retro_mmur_1563,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Macaca mulatta	ENSMMUG00000005524	2 retrocopies	retro_mmul_668, retro_mmul_991,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Mus musculus	ENSMUSG00000031683	2 retrocopies	retro_mmus_820, retro_mmus_956,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Pongo abelii	ENSPPYG00000015105	1 retrocopy	retro_pabe_1994,
Pan troglodytes	ENSPTRG00000016488	1 retrocopy	retro_ptro_1545,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,
Tarsius syrichta	ENSTSYG00000006837	4 retrocopies	retro_tsyr_1239, retro_tsyr_1782, retro_tsyr_192, retro_tsyr_2115,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340 , retro_tsyr_653,