RetrogeneDB ID: retro_tsyr_2119

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_92844:1..1455(+)
• 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_2119
CTTGCTGCGACCATGTTCATCAGTCAGGGGATTCCTGTATACCTCTTTTCTGGCATAACCCCAACCCCTTTGTGCCCTAC
ACAGTATCACATCTGAAACTCTGTGCGGGGATCATGGACACCGCTTCCCACAACCCGAAGCAAGATAATAGCTACAAGGT
CTACTGGGATAAGGGAGCTCAGATCATCTCTCCTCATGACAAAGGGATTTCTCAAGCTATTGAAGAAAATCTAGAGCCAT
GGCCTCAAGCTTGGGACGACTCTTCAATTGATGACAGCCCACTGCTGCACGACCCAAATGCTTCCATCAATAACGACTAC
TTTGAAGACCTTAAAAAATACTGTTTCCACAGGAGTGTGAACAGAGAGACCAAGGTGAAGTTCGTGCACACCTTCGTCCA
CGGGGTGGGGCATAACTTCGTGCAGTCGGCTTTCAAGGCTTTTGACCTTGTTCCTCCTGAGGCCGTGTCCAAGCAGAAAG
ATCCTGATCCTGAGTTCCCGAGAGTGAAATACCCAAATCCCGAAGAGGGTAAAGGTGTCTTGACTTCGTCTTTTGCTTTC
GCTGACAAAACCAAAACTAAAATTGTGCTAGCAAATGACCCAGATGCGGATAGACTTGCTGTGGCAGAAAAGCAAGACAG
TGGTGAATGGAGAGTGTTTTCAGGCAATGAGTTGGGGGCGCTCCTGGGCTGGTGGCTTTTTACTTCTTGGAAAGAAAAGA
ACAAGGACCGCAGTGCCCTCAAAGACACCTACATGTTGTCTAGCACCGTCTCCTCCAAAATCCTGCGTGCCATCGCCTTA
ACGGAGGGTTTCCATATCGAGGAAACATTAACTGGCTTTAAGTGGATGGGTATCAGAGCCAAGCAGCTGCTAGACCAGGG
AAAAACTGTCTTGTTTGCATTTGAGGAAGCTATGGGATATATGTGCTGCCCTTTTGTCCTGGACAAAGATGGAGTCAGTG
CCGCTGTCATAGGCGCAGAGCTGGCCAGTTTTCTAGCTACCAAGAATCTTTCTATGTCTCAGCAGCGTAAGGCCATCTAC
ATGGAGTATGGCTATCACCTTACCAAAGCTTTCTGTTTTATCTGATATGATCAAACCATTATTGAAACATTATTTGAAAA
CCTCCGAAACTACGATGGAAAAAATCACTATCCAAAAATGTGTGGCAGATTTGAAATATCTGCCATTAGGGACCTCACCA
CTGCCTATGATGACAGCCAACCTGATAAAAAGGCTGTTCTTCCCACGAGTAAAAGCAGCCAAATGATAACATTCACCTTT
GCCAATGGAGGAGTGGCCACCATGCGAACCAGTGGGACTGAGCCCAAAATCAAGTACTACACAGAACTGTGTGCCCCTCC
TGGAAACAGTGACCCTGAGCAGCTGAAGAAGGAACTGAATGAACTAGTCAGTGCGATTGAAGAACATTTTTTCCAGGCAC
AAAAGTACAATTTG

Alignment

ORF - retro_tsyr_2119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.93 %
• Parental protein coverage: 82.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTAAVLLAKDVPVYLFSRYVPTP-FVPYAVQELKAVAGVMITASHNRKEDNGYKVYWETGAQITSPHDKE
          L.A........PVYLFS...PTP.FVPY.V..LK..AG.M.TASHN.K.DN.YKVYW..GAQI.SPHDK.
Retrocopy LAATMFISQGIPVYLFSGITPTP<FVPYTVSHLKLCAGIMDTASHNPKQDNSYKVYWDKGAQIISPHDKG

Parental  ILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQDICRRYMEDLKKICFYRELNSKTTLKFVHTSFHGVGHD
          I...IEE..EPW...W.D...D.SPL..DP...I...Y.EDLKK.CF.R..N..T..KFVHT..HGVGH.
Retrocopy ISQAIEENLEPWPQAWDDSSIDDSPLLHDPNASINNDYFEDLKKYCFHRSVNRETKVKFVHTFVHGVGHN

Parental  YVQLAFQVFGFRPPIPVPEQKDPDPEFSTVKCPNPEEGESVLELSLRLAEKENARIVLATDPDADRLAVA
          .VQ.AF..F...PP..V..QKDPDPEF..VK.PNPEEG..VL..S...A.K....IVLA.DPDADRLAVA
Retrocopy FVQSAFKAFDLVPPEAVSKQKDPDPEFPRVKYPNPEEGKGVLTSSFAFADKTKTKIVLANDPDADRLAVA

Parental  ELQENGHWKVFTGNELAALFGWWMFDCWR-KNKPRNADVKNIYMLATTVSSKILKAIAFKEGFHFEETLP
          E.Q..G.W.VF.GNEL.AL.GWW.F..W..KNK.R.A..K..YML..TVSSKIL.AIA..EGFH.EETL.
Retrocopy EKQDSGEWRVFSGNELGALLGWWLFTSWKEKNKDRSA-LKDTYMLSSTVSSKILRAIALTEGFHIEETLT

Parental  GFKWIGSRIKDLLENGKEVLFAFEESIGFLCGTSVLDKDGVSAAVVVAEMASYLETMNVTLKQQLIKVYE
          GFKW.G.R.K.LL..GK.VLFAFEE..G..C...VLDKDGVSAAV..AE.AS.L.T.N....QQ....Y.
Retrocopy GFKWMGIRAKQLLDQGKTVLFAFEEAMGYMCCPFVLDKDGVSAAVIGAELASFLATKNLSMSQQRKAIYM

Parental  KYGYHISKTSYFLCYDPLTIKSIFERLRNFDSPKEYPKFCGTFAILHVRDITTGYDSSQPNKKSVLPVSK
          .YGYH..K...F..YD...I...FE.LRN.D....YPK.CG.F.I...RD.TT.YD.SQP.KK.VLP.SK
Retrocopy EYGYHLTKAFCFI*YDQTIIETLFENLRNYDGKNHYPKMCGRFEISAIRDLTTAYDDSQPDKKAVLPTSK

Parental  NSQMITFTFQNGCVATLRTSGTEPKIKYYAEMCASPDQSDTALLEEELKKLIEALIENFLQPSKNGL
          .SQMITFTF.NG.VAT.RTSGTEPKIKYY.E.CA.P..SD...L..EL..L..A..E.F.Q..K..L
Retrocopy SSQMITFTFANGGVATMRTSGTEPKIKYYTELCAPPGNSDPEQLKKELNELVSAIEEHFFQAQKYNL

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_2119 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,