RetrogeneDB ID: retro_tsyr_2112

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_92371:1012..2742(-)
• 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_2112
ACGTTGGAGTCCGTGAAGCGACTGGTAGCAGAAGGCAATGAAGAAGAGCTGCACAGATGTTTTGGGGCCCGGATGGAGGT
CGAGACAGCTGGCCTGCGAGCTGCCATGGGAGTAGGAACCTCCTGCATGAACGACTTGACCATCATCCAGACTACGCAGG
GATTTTGCAGATACCTGGAAAAACAATTCAGTGACCCGAAGCAGAGAGGTGTCGTGATCAGCTTTGACTCACGGGCCCAT
CCTCCCAGTGGCGGCAGCAGCCGCAGGTTTGCCCGACTTGCTGCGACCATGTTCATCAGTCAGGGGATTCCTGTATACCT
CTTTTCTGGCATAACCCCAACCCCTTTGTGCCCTACACAGTATCACATCTGAAACTCTGTGCGGGGATCATGGACACCGC
TTCCCACAACCCGAAGCAAGATAATAGCTACAAGGTCTACTGGGATAAGGGAGCTCAGATCATCTCTCCTCATGACAAAG
GGATTTCTCAAGCTATTGAAGAAAATCTAGAGCCATGGCCTCAAGCTTGGGACGACTCTTCAATTGATGACAGCCCACTG
CTGCACGACCCAAATGCTTCCATCAATAACAACTACTTTGAAGACCTTAAAAAATACTGTTTCCACAGGAATGTGAACAG
AGAGACCAAGGTGAAGTTCGTGCACACCTTCGTCCACGGGGTGGGGCATAACTTCGTGCAGTCGGCTTTCAAGGCTTTTG
ACCTTGTTCCTCCTGAGGCCGTGTCCAAGCAGAAAGATCCTGATCCTGAGTTCCCGAGAGTGAAATACCCCAATCCCGAA
GAGGGTAAAGGTGTCTTGACTTCGTCTTTTGCTTTCGCTGACAAAACCAAACCTAAAATTGTGCTAGCAAATGACCCAGA
TGCGGATAGACTTGCTGTGGCAGAAAAGCAAGACAGTGGTGAATGGAGAGTGTTTTCAGGCAATGAGTTGGGGGTGCTCC
TGGGCTGGTGGCTTTTTACTTCTTGGAAAGAAAAGAACAAGGACCGCAGTGCCCTCAAAGACACCTACATGTTGTCTAGC
ACCGTCTCCTCCAAAATCCTGCGTGCCATCGCCTTAACGGAGGGTTTCCATATCGAGGAAACATTAACTGGCTTTAAGTG
GATGGGTAACAGAGCCAAGCAGCTGCTAGACCAGGGAAAAACTGTCTTGTTTGCATTTGAGGAAGCTATGGGATATATGT
GCTGCCCTTTTGTCCTGGACAAAGATGGAGTCAGTGCCGCTGTCATAGGCGCAGAGCTGGCCAGTTTTCTAGCTACCAAG
AATCTTTCTATGTCTCAGCAGCGTAAGGCCATCTACATGGACTATGGCTATCACCTTACCAAAGCTTTCTGTTTTATCTG
ACATGATCAAACCATCATTGAAACATTATTTGAAAACCTCCGAAACTACGATGGAAAAAATCACTATCCAAAAATGTGTG
GCAGATTTGAAATATCTGCCATTAGGGACCTCACCACTGGCTATGGCGACAGCCAACCTGATAAAAAGGCTGTTCTTCCC
ACGAGTAAAAGCAGCCAAATGAAAACATTCACCTTTGCCAGTGGAGGAATAGCCACCATGTGGACCAGTGGGATGGAGCC
CCAAATCAAGCTCTACACAGAACTGTGTGCCCCTCATGGAAACAGTGATCCTGAGTAGCTGAAGAAGGAACTGAGTGAAC
TAGTCAGTGCGATTGAAGAACATTTTTTCCAGCCAAAAAAGGACAATCTG

Alignment

ORF - retro_tsyr_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.61 %
• Parental protein coverage: 98.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKEQIENLLRNGMNKELRDRLCCRMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFKQRG
          T.E....L...G...EL......RM...TAGLR.AMG.G....NDLT.IQ.TQG...YLE..FSD.KQRG
Retrocopy TLESVKRLVAEGNEEELHRCFGARMEVETAGLRAAMGVGTSCMNDLTIIQTTQGFCRYLEKQFSDPKQRG

Parental  FVVGYDTRGQVTSSCSSQRLAKLTAAVLLAKDVPVYLFSRYVPTP-FVPYAVQELKAVAGVMITASHNRK
          .V...D.R....S..SS.R.A.L.A........PVYLFS...PTP.FVPY.V..LK..AG.M.TASHN.K
Retrocopy VVISFDSRAHPPSGGSSRRFARLAATMFISQGIPVYLFSGITPTP<FVPYTVSHLKLCAGIMDTASHNPK

Parental  EDNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQDICRRYMEDLKKICFY
          .DN.YKVYW..GAQI.SPHDK.I...IEE..EPW...W.D...D.SPL..DP...I...Y.EDLKK.CF.
Retrocopy QDNSYKVYWDKGAQIISPHDKGISQAIEENLEPWPQAWDDSSIDDSPLLHDPNASINNNYFEDLKKYCFH

Parental  RELNSKTTLKFVHTSFHGVGHDYVQLAFQVFGFRPPIPVPEQKDPDPEFSTVKCPNPEEGESVLELSLRL
          R..N..T..KFVHT..HGVGH..VQ.AF..F...PP..V..QKDPDPEF..VK.PNPEEG..VL..S...
Retrocopy RNVNRETKVKFVHTFVHGVGHNFVQSAFKAFDLVPPEAVSKQKDPDPEFPRVKYPNPEEGKGVLTSSFAF

Parental  AEKENARIVLATDPDADRLAVAELQENGHWKVFTGNELAALFGWWMFDCWR-KNKPRNADVKNIYMLATT
          A.K....IVLA.DPDADRLAVAE.Q..G.W.VF.GNEL..L.GWW.F..W..KNK.R.A..K..YML..T
Retrocopy ADKTKPKIVLANDPDADRLAVAEKQDSGEWRVFSGNELGVLLGWWLFTSWKEKNKDRSA-LKDTYMLSST

Parental  VSSKILKAIAFKEGFHFEETLPGFKWIGSRIKDLLENGKEVLFAFEESIGFLCGTSVLDKDGVSAAVVVA
          VSSKIL.AIA..EGFH.EETL.GFKW.G.R.K.LL..GK.VLFAFEE..G..C...VLDKDGVSAAV..A
Retrocopy VSSKILRAIALTEGFHIEETLTGFKWMGNRAKQLLDQGKTVLFAFEEAMGYMCCPFVLDKDGVSAAVIGA

Parental  EMASYLETMNVTLKQQLIKVYEKYGYHISKTSYFLCYDPLTIKSIFERLRNFDSPKEYPKFCGTFAILHV
          E.AS.L.T.N....QQ....Y..YGYH..K...F...D...I...FE.LRN.D....YPK.CG.F.I...
Retrocopy ELASFLATKNLSMSQQRKAIYMDYGYHLTKAFCFI*HDQTIIETLFENLRNYDGKNHYPKMCGRFEISAI

Parental  RDITTGYDSSQPNKKSVLPVSKNSQMITFTFQNGCVATLRTSGTEPKIKYYAEMCASPDQSDTALLEEEL
          RD.TTGY..SQP.KK.VLP.SK.SQM.TFTF..G..AT..TSG.EP.IK.Y.E.CA....SD...L..EL
Retrocopy RDLTTGYGDSQPDKKAVLPTSKSSQMKTFTFASGGIATMWTSGMEPQIKLYTELCAPHGNSDPE*LKKEL

Parental  KKLIEALIENFLQPSKNGL
          ..L..A..E.F.QP.K..L
Retrocopy SELVSAIEEHFFQPKKDNL

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_2112 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,