RetrogeneDB ID: retro_tsyr_1740

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_564122:11..915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGM2L1
• Ensembl ID: ENSTSYG00000002928
• Aliases: None
• Description: phosphoglucomutase 2-like 1 [Source:HGNC Symbol;Acc:20898]

Sequence

>retro_tsyr_1740
CGGATGGAGGTCGAGACAGCTGGCCTGCGAGCTGCCATGGGAGTAGGAACCTCCTGCATGAACGACTTGACCATCATCCA
GACTACGCAGGGATTTTGCAGATACCTGGAAAAACAATTCAGTGACCCGAAGCAGAGAGGTGTCGTGATCAGCTTTGACG
CACGGGCCCATCCTCCCAGTGGCGGCAGCAGCCGCAGGTTTGCCCGACTTGCTGCGACCATGTTCATCAGTCAGGGGATT
CCTGTATACCTCTTTTCTGGCATAACCCCAACCCCTTTGTGCCCTACACAGTATCACATCTGAAACTCTGTGCGGGGATC
ATGGACACCGCTTCCCACAACCCGAAGCAAGATAATAGCTACAAGGTCTACTGGGATAAGGGAGCTCAGATCATCTCTCC
TCATGACAAAGGGATTTCTCAAGCTATTGAAGAAAATCTAAAGCCATGGCCTCATGCTTGGGACGACTCTTCAATTGATG
GCAGCCCACTGCTGCACGACCCAAATGCTTCCATCAATAACAACTACTTTGAAGACCTTAAAAAATACTGTTTTCACAGG
AGTGTGAACACAGAGACCAAGGTGAAGTTCATGCACCCTTCGTCCACGGGGTGGGGCATAACATCGTGCAGTCGGCTTTC
AAGGCTTTTGACCTTGTTCCTCCTGAGGCCGAGTCCAAGCAGAAAGATCCTGATCCTGAGTTCACGAGAGTGAAATACCC
AAATCCCGAAGAGGGTAAAGGTGTCTTGACTTTGTCTTTTGCTTTGGCTGACAAAACCAAAACTAAAATTGTGCTAGCAA
ATGACCCAGATGCGGATAGACTTGCTGTGGCAGAAAAACAAGTCAGTGGTGAATGGAGAGTGTTTTCAGGCAATGAGTTG
GGGGCGCTCCTGGGCTGGTGGATT

Alignment

ORF - retro_tsyr_1740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.57 %
• Parental protein coverage: 51.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFKQRGFVVGYDTRGQVTSSCSSQRLAKL
          RM...TAGLR.AMG.G....NDLT.IQ.TQG...YLE..FSD.KQRG.V...D.R....S..SS.R.A.L
Retrocopy RMEVETAGLRAAMGVGTSCMNDLTIIQTTQGFCRYLEKQFSDPKQRGVVISFDARAHPPSGGSSRRFARL

Parental  TAAVLLAKDVPVYLFSRYVPT-PFVPYAVQELKAVAGVMITASHNRKEDNGYKVYWETGAQITSPHDKEI
          .A........PVYLFS...PT.PFVPY.V..LK..AG.M.TASHN.K.DN.YKVYW..GAQI.SPHDK.I
Retrocopy AATMFISQGIPVYLFSGITPT<PFVPYTVSHLKLCAGIMDTASHNPKQDNSYKVYWDKGAQIISPHDKGI

Parental  LKCIEECVEPWNGSWNDNLVDTSPLKRDPLQDICRRYMEDLKKICFYRELNSKTTLKFVHTS-FHGVGHD
          ...IEE...PW...W.D...D.SPL..DP...I...Y.EDLKK.CF.R..N..T..KF.H.S..HGVGH.
Retrocopy SQAIEENLKPWPHAWDDSSIDGSPLLHDPNASINNNYFEDLKKYCFHRSVNTETKVKFMHPS<VHGVGHN

Parental  YVQLAFQVFGFRPPIPVPEQKDPDPEFSTVKCPNPEEGESVLELSLRLAEKENARIVLATDPDADRLAVA
          .VQ.AF..F...PP.....QKDPDPEF..VK.PNPEEG..VL.LS..LA.K....IVLA.DPDADRLAVA
Retrocopy IVQSAFKAFDLVPPEAESKQKDPDPEFTRVKYPNPEEGKGVLTLSFALADKTKTKIVLANDPDADRLAVA

Parental  ELQENGHWKVFTGNELAALFGWWM
          E.Q..G.W.VF.GNEL.AL.GWW.
Retrocopy EKQVSGEWRVFSGNELGALLGWWI

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_1740 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 2 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009209	1 retrocopy	retro_chof_557,
Tarsius syrichta	ENSTSYG00000002928	7 retrocopies	retro_tsyr_1740 , retro_tsyr_1839, retro_tsyr_2095, retro_tsyr_2112, retro_tsyr_2119, retro_tsyr_721, retro_tsyr_849,