RetrogeneDB ID: retro_tsyr_2000

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_7732:35303..35675(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000008082
• Aliases: None
• Description: None

Sequence

>retro_tsyr_2000
AATGTCACAGGTAGATTAATGGTGAGTCTACATTGTTGGAATTGCATTGATGAAGATGAAAAGAGCCCTTAGGTGTTTGA
GTCCAAGAAAGTTTTCTCTCAAAAGAATAAAACTGTTTCAGAGGCTGTTTCAGGAATCATTTGGTTGGAATTTATTGCCT
GCCCAATACTGTGGGTGATATGTGCCTTTAATGTCCTCTTACCCTTCAGAATAAAGTGGTTGTTGGTGGTTATCATGGGT
GCGGTACTACAAGGTGCCAACTTATATGGTTACATTAGTTAGGAGGCAGACAGTAGAAAGAATTTAACCAACAGGATATG
TCGCATCTTGAAGGAGTTTTTAAGACAAAACACTGGAGATGATCATACTTCT

Alignment

ORF - retro_tsyr_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.6 %
• Parental protein coverage: 60.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVTGRLMVGLRWWNHIDEDGKSHWVFESRKASSQENKNISEAEARIFWLGLIACPVLWVIFAFSALFSFR
          NVTGRLMV.L..WN.IDED.KS..VFES.K..SQ.NK..SEA...I.WL..IACP.LWVI.AF..L..FR
Retrocopy NVTGRLMVSLHCWNCIDEDEKSP*VFESKKVFSQKNKTVSEAVSGIIWLEFIACPILWVICAFNVLLPFR

Parental  VKWLAVVIMGVVLQGANLYGYIRCKVGSRKNLTSMATSYLGKQFLKQNTGDDQTS
          .KWL.VVIMG.VLQGANLYGYI.....SRKNLT......L.K.FL.QNTGDD.TS
Retrocopy IKWLLVVIMGAVLQGANLYGYIS*EADSRKNLTNRICRIL-KEFLRQNTGDDHTS

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_2000 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Homo sapiens	ENSG00000171928	1 retrocopy	retro_hsap_2278,
Homo sapiens	ENSG00000175106	1 retrocopy	retro_hsap_1625,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Macaca mulatta	ENSMMUG00000019203	5 retrocopies	retro_mmul_1032, retro_mmul_2125, retro_mmul_278, retro_mmul_600, retro_mmul_748,
Nomascus leucogenys	ENSNLEG00000014658	2 retrocopies	retro_nleu_1961, retro_nleu_2008,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Pan troglodytes	ENSPTRG00000007790	1 retrocopy	retro_ptro_20,
Pan troglodytes	ENSPTRG00000008796	1 retrocopy	retro_ptro_996,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000 , retro_tsyr_530,