RetrogeneDB ID: retro_tsyr_308

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_7720:52433..52998(+)
• Located in intron of: ENSTSYG00000004287

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR3
• Ensembl ID: ENSTSYG00000000166
• Aliases: None
• Description: proline rich 3 [Source:HGNC Symbol;Acc:21149]

Sequence

>retro_tsyr_308
ATGCTGAAACAAAAGAAGCAGAATCAGCACCAGCCACCCTCACTGCAGCAGCCCCCACTGCCTGAGCAGGAAGAGACTGG
AGATGAGGAGGATGAGAATCCCATCAGACCACCCAACCTTCTGGGCCCTCCCACAATGGCCAATGGAAAGCCTGGTGATC
CCAAGTCAGCTCTTCACAGAGGTCCTCCTGGATCAAGGGGACCAATGATTCTACCACTGCTGAGTCTCCCACCTCTTCCT
TGGGGTAGAGGTCCAATTCGGGGAGACTTTGGCCTCAGGCCTGGCCCATATGATTGTGGTTGGTGGGGGCATCAGTGCTG
AATCTCCTTTTCTGGGGCCAGGCCATAGTGGTCCCTCCAGGGGAAGCTTTCACAAAGAGCAGAGAAATCCTCCAAGACTC
AAAAGTTGATCTCTTATCAAGAATACTTGCCCACCCAAGGATGATCCCCAGGTTATAGAAGACAAATCTGGCAGCCCTGT
CTGCCAACACTTTGCCAAAAAGGGCCACTGTCGATATGAGGACCTTTGTGCCTTCTACCACCCAGGCGTCAATGGACCTC
CTCTG

Alignment

ORF - retro_tsyr_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKKQNQHQPLPPQQPPLPERGETGDEEDENPIGPPSLLGPPPMANGKPGDPKSVLYRGTPGPRGPMI
          M.K.KKQNQHQP...QQPPLPE..ETGDEEDENPI.PP.LLGPP.MANGKPGDPKS.L.RG.PG.RGPMI
Retrocopy MLKQKKQNQHQPPSLQQPPLPEQEETGDEEDENPIRPPNLLGPPTMANGKPGDPKSALHRGPPGSRGPMI

Parental  PPLLSLPPPPRGRASIRGGFGPRSGPYGRGWWG-VSAEPPFPGPGHGGPSRGSFHKEQRNPRRLKSWSLI
          .PLLSLPP.P.GR..IRG.FG.R.GPY..GWWG..SAE.PF.GPGH.GPSRGSFHKEQRNP.RLKS.SLI
Retrocopy LPLLSLPPLPWGRGPIRGDFGLRPGPYDCGWWG>ISAESPFLGPGHSGPSRGSFHKEQRNPPRLKS*SLI

Parental  KNTCPPKDDPQVIEDKSGRPVCRHFAKKGHCRYEDLCAFYHPGVNGPPL
          KNTCPPKDDPQVIEDKSG.PVC.HFAKKGHCRYEDLCAFYHPGVNGPPL
Retrocopy KNTCPPKDDPQVIEDKSGSPVCQHFAKKGHCRYEDLCAFYHPGVNGPPL

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_308 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308 , retro_tsyr_841,