RetrogeneDB ID: retro_tsyr_1956

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_715:76335..76857(+)
• Located in intron of: ENSTSYG00000004496

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000005812
• Aliases: None
• Description: None

Sequence

>retro_tsyr_1956
AACCTGCTCCTGCAAAAGTGGAGGCGAAGGCAAAAAAAGGCGACAGTAAAGGATAAGTCTTCAGACAAAAAAGTGCCAGC
AAAAGGGAAAAGGGGAGCAAAGGGAAAACAGGCTGAAGGGCTAACCAAGAAAATAAAGAGTTACCTGAAGAAAACGGAGA
AACGAAAACCGAGAATCCACCCTCTTGGGGTAGCAGGAGAGAAAAAAAAGCCAAGTCTGAATATCATCTACCATGTCTTA
TCAGTGATGTCTCCCTTCTTGAACAATCCAGAGGAATATTTTTATCAACTATTTTGTAAATGCAAATTTTTTAGTAGCTC
TTGAAACATTTTTAGGAGGAGGGAATCCCACCTCATCCCATTTTTTAAGTGTAAAGTTCACCTCTTAAGAGGTGAGATCG
TTCCCTGGTAGTTTATTCTTTGGTACAATCAGAAAACAGTGTGGGATACTGGATTACAGGAGGTTTTGACTGTCTTGGGT
GTCTTAACATTTCAGAGATGGAGGCTTCGTTTTTACATTCTA

Alignment

ORF - retro_tsyr_1956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NLLLQKWKQSQK-RRRERINLQTKKCKQKGKGERRESRLK-WLTKKLKKSYLQKMEKLKPRRIQPL-MKQ
          NLLLQKW...QK.RR..RI.LQTKKC.QKGKGE.RE.RLK..LTKK..KSYL.K.EK.KP.RI.PL....
Retrocopy NLLLQKWRRRQK>RRQ*RISLQTKKCQQKGKGEQRENRLK<GLTKKI-KSYLKKTEKRKP-RIHPLGVAG

Parental  ERKKPSLN-NHIPCLISGPCLPSCTIQRNIFIN-YFVNASFLVALETFLRRRESHLIPFFKCKCFFLRGE
          E...PSLN..H.PCLIS...L......R.IF....F....F........RRRESHLIPFFKCK...LRGE
Retrocopy EXXXPSLN<YHLPCLISDVSL--LEQSRGIFLS>LFCKCKFFSSS*NIFRRRESHLIPFFKCKVHLLRGE

Parental  IIRWLFIFWYNQKIVWDIELQEALTVLSISLTFHRWGVSFYIL
          I..W.FI.WYNQK.VWD..LQE.LTVL...LTF.RW...FYIL
Retrocopy IVPW*FILWYNQKTVWDTGLQEVLTVLGV-LTFQRWRLRFYIL

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_1956 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 6 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005727	4 retrocopies	retro_cjac_1105, retro_cjac_1412, retro_cjac_2018, retro_cjac_4230,
Gorilla gorilla	ENSGGOG00000013672	6 retrocopies	retro_ggor_107, retro_ggor_145, retro_ggor_16, retro_ggor_2248, retro_ggor_48, retro_ggor_49,
Otolemur garnettii	ENSOGAG00000033084	3 retrocopies	retro_ogar_1799, retro_ogar_2793, retro_ogar_3104,
Tarsius syrichta	ENSTSYG00000005812	15 retrocopies	retro_tsyr_1029, retro_tsyr_1109, retro_tsyr_1203, retro_tsyr_1209, retro_tsyr_1243, retro_tsyr_1318, retro_tsyr_1904, retro_tsyr_1956 , retro_tsyr_310, retro_tsyr_399, retro_tsyr_652, retro_tsyr_664, retro_tsyr_680, retro_tsyr_728, retro_tsyr_913,
Tursiops truncatus	ENSTTRG00000015372	12 retrocopies	retro_ttru_1034, retro_ttru_129, retro_ttru_1511, retro_ttru_1682, retro_ttru_1714, retro_ttru_200, retro_ttru_337, retro_ttru_373, retro_ttru_558, retro_ttru_61, retro_ttru_680, retro_ttru_980,
Vicugna pacos	ENSVPAG00000000013	7 retrocopies	retro_vpac_146, retro_vpac_216, retro_vpac_248, retro_vpac_371, retro_vpac_499, retro_vpac_557, retro_vpac_66,