RetrogeneDB ID: retro_tsyr_1839

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_61689:3937..5675(-)
• 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_1839
AATCCTTTAACGTTGGAGTCCGTGAAGCGACTGGTAGCAGAAGGCAATGAAGAAGAGCTGCACAGATGTTTTGGGGCCCG
GATGGAGGTCGAGACAGCTGGCCTGCGAGCTGCCATGGGAGTAGGAACCTCCTGCATGAACGACTTGACCATCATCCAGA
CTACGCAGGGATTTTGCAGATACCTGGAAAAACAATTCAGTGACCCGAAGCAGAGAGGTGTCGTGATCAACTTTGACGCA
CGGGCCCATCCTCCCAGTGGCGGCAGCAGCTGAAGGTTTGCCCGACTTGCTGCGACCATGTTCATCAGTCAGGGGATTCC
TGTATACCTCTTTTCTGGCATAACCCCAACCCCTTTGTGCCCTACACAGTATCACATCTGAAACTCTGTGCGGGGATCAT
GGACACCGCTTCCCACAACCCGAAGCAAGATAATAGCTACAAGGTCTACTGGGATAAGGGAGCTCAGATCATCTCTCCTC
ATGACAAAGGGATTTCTCAAGCTATTGAAGAAAATCTAGAGCCATGGCCTCAAGCTTGGAACGACTCTTCAATTGATGAC
AGCCCACTGCTGCACGACCCAAATGCTTCCATCAATAACGACTACTTTGAAGACCTTAAAAAATACTGTTTCCACAGGAA
TGTGAACAGAGAGACCAAGGTGAAGTTCGTGCACACCTTCGTCCACGGGGTGGGGCATAACTTCGTGCAGTCGGCTTTCA
AGGCTTTTGACCTTGTTCCTCCTGAGGCCGTGTCCAAGCAGAAAGATCCTGATCCTGAGTTCCCGAGAGTGAAATACCCA
TATCCAGAAGAGGGTAAAGGTGTCTTGACTTCGTCTTTTGCTTTCACTGACAAAACCAAAACTAAAATTGTGCTAGCAAA
TGACCCAGATGCGGATAGACTTGCTGTGGCAGAAAAGCAAGACAGTGGTGAATGGAGAGTGTTTTCAGGCATGAGTTGGG
GGCGCTCCTGTGTTGGTGGCTTTTTACTTCTTGGAAAGAAAAGAACAAGGACCGCAGTGCCCTCAAAGACACCTACATGT
TGTCTAGCACCGTCTCCTCCAAAATCCTGCGTGCCATCGCCTTAACGGAGGGTTTCCATATCGAGGAAACATTAACTGGT
TTTAAGTGGATGGGTAACAGAGCCAAGCAGCTGCTAGACCAGGGAAAAACTGTCTTGTTTGCATTTGAGGAAGCTATTGG
ATATATGTGCTGCCCTTTTGTCCAGGACAAAGATGGAGTCAGTGCCGCTGTCATAGGCGCAGAGCTGGCCAGTTTTCTAG
CTACCAAGAACCTTTTATGTCTCACCAGCTGAAGGCCATCTACATGGAGTATGGCTATCATCTTACCAAAGCTTTCTGTT
TTATCTGATATGATCAAACCATTATTGAAACATTATTTGAAAACCTCCGAAACTACGATGGGAAAAAATCACTATCCAAA
AATGTGTGGCAGATTTGAAATATCTGCCATTAGGGACCTCACCACTGGCTATGGCGACAGCCAACCTGATAAAAAGGCTG
TTCTTCCCACGAGTAAAAGCAGCCAAATGATAACATTCACCTTTGCCAATGGAGGAGTGGCCACCATGCGAACCAGTGGG
ACTGAGCCCAAAATCAAGTACTACACAGAACTGTGTGCCCCTCCTGGAAACAGTGACCCTGAGCAGCTGAAGAAGGAACT
GAATGAACTAGTCAGTGCGATTGAAGAACATTTTTTCCAGGCACAAAAGTACAATTTG

Alignment

ORF - retro_tsyr_1839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.58 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NPKTKEQIENLLRNGMNKELRDRLCCRMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFK
          NP.T.E....L...G...EL......RM...TAGLR.AMG.G....NDLT.IQ.TQG...YLE..FSD.K
Retrocopy NPLTLESVKRLVAEGNEEELHRCFGARMEVETAGLRAAMGVGTSCMNDLTIIQTTQGFCRYLEKQFSDPK

Parental  QRGFVVGYDTRGQVTSSCSSQRLAKLTAAVLLAKDVPVYLFSRYVPTP-FVPYAVQELKAVAGVMITASH
          QRG.V...D.R....S..SS.R.A.L.A........PVYLFS...PTP.FVPY.V..LK..AG.M.TASH
Retrocopy QRGVVINFDARAHPPSGGSS*RFARLAATMFISQGIPVYLFSGITPTP<FVPYTVSHLKLCAGIMDTASH

Parental  NRKEDNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQDICRRYMEDLKKI
          N.K.DN.YKVYW..GAQI.SPHDK.I...IEE..EPW...WND...D.SPL..DP...I...Y.EDLKK.
Retrocopy NPKQDNSYKVYWDKGAQIISPHDKGISQAIEENLEPWPQAWNDSSIDDSPLLHDPNASINNDYFEDLKKY

Parental  CFYRELNSKTTLKFVHTSFHGVGHDYVQLAFQVFGFRPPIPVPEQKDPDPEFSTVKCPNPEEGESVLELS
          CF.R..N..T..KFVHT..HGVGH..VQ.AF..F...PP..V..QKDPDPEF..VK.P.PEEG..VL..S
Retrocopy CFHRNVNRETKVKFVHTFVHGVGHNFVQSAFKAFDLVPPEAVSKQKDPDPEFPRVKYPYPEEGKGVLTSS

Parental  LRLAEKENARIVLATDPDADRLAVAELQENGHWKVFTG-NELAALFGWWMFDCWR-KNKPRNADVKNIYM
          .....K....IVLA.DPDADRLAVAE.Q..G.W.VF.G..EL.AL..WW.F..W..KNK.R.A..K..YM
Retrocopy FAFTDKTKTKIVLANDPDADRLAVAEKQDSGEWRVFSG<HELGALLCWWLFTSWKEKNKDRSA-LKDTYM

Parental  LATTVSSKILKAIAFKEGFHFEETLPGFKWIGSRIKDLLENGKEVLFAFEESIGFLCGTSVLDKDGVSAA
          L..TVSSKIL.AIA..EGFH.EETL.GFKW.G.R.K.LL..GK.VLFAFEE.IG..C...V.DKDGVSAA
Retrocopy LSSTVSSKILRAIALTEGFHIEETLTGFKWMGNRAKQLLDQGKTVLFAFEEAIGYMCCPFVQDKDGVSAA

Parental  VVVAEMASYLETMNVT-LKQQLIKVYEKYGYHISKTSYFLCYDPLTIKSIFERLRNFDSPK-EYPKFCGT
          V..AE.AS.L.T.N......QL...Y..YGYH..K...F..YD...I...FE.LRN.D..K..YPK.CG.
Retrocopy VIGAELASFLATKNLL<MSHQLKAIYMEYGYHLTKAFCFI*YDQTIIETLFENLRNYDGKK>HYPKMCGR

Parental  FAILHVRDITTGYDSSQPNKKSVLPVSKNSQMITFTFQNGCVATLRTSGTEPKIKYYAEMCASPDQSDTA
          F.I...RD.TTGY..SQP.KK.VLP.SK.SQMITFTF.NG.VAT.RTSGTEPKIKYY.E.CA.P..SD..
Retrocopy FEISAIRDLTTGYGDSQPDKKAVLPTSKSSQMITFTFANGGVATMRTSGTEPKIKYYTELCAPPGNSDPE

Parental  LLEEELKKLIEALIENFLQPSKNGL
          .L..EL..L..A..E.F.Q..K..L
Retrocopy QLKKELNELVSAIEEHFFQAQKYNL

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_1839 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,