RetrogeneDB ID: retro_tsyr_543

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_136933:3680..4759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LARP1
• Ensembl ID: ENSTSYG00000013732
• Aliases: None
• Description: La ribonucleoprotein domain family, member 1 [Source:HGNC Symbol;Acc:29531]

Sequence

>retro_tsyr_543
GGCCGGGACCGCGGCCGGGGTGGCACTCGAACCCATTTTGGCTACCAGTTTGGCTACCGGAAGTTTGATGGTACAGAGGG
GCCTCGCACCTCCAAGTACATGAACAATATCACCGACTGCTTTGACAATGTCAGCAGCACCGAGCTGTACAGCGTGGACC
AGGAGCTGCTCAAAGACCACGTCAAGCGCCAGACTGAGTACTACTTCAGCGTGGACACTTTAGAGCCAGACTTTTTCCTG
CGACGGAAGATGGATGCGGATGGCTTCCTACCATCACCCTTACTGCCTCCTTCCACCGAGGGCAGGCTCTTACCACTGAC
ATTTCACTCCTCTTTGCGGCCCTGAAAGACAGCCAGGTGGTGGAGATCGTTGACGAGAAAGTTCGTAGAAGGGAGGAGCC
TGAGAAGTGGCCTCTTCCTGGGCCCCCAATAGTGGATTATTCACAGACTGATTTCCCCCAGCTGCTCAACTGCCCTGAGT
TTGTCCCCTGCTAGCACTACCAAAAGGAGACAGAGTCGGCCCCTGGCTCTCCGCGTGCAGCCACCCCAGTGCCAACCAAA
ACAGAAGAGGTCAGCAACCTAAAGACACTGCCCAAGGGCCTGTCTGCCAGCCTGCCTGACCTGGATTCCAAGGAATGGAT
TGAAGTGAAGAAGCGGCCTCGGCCCTCGCCAGCACGGCCCAAGAAATCAGAGGAGCCCAGGTTTGCCCGCCCAACCTCTC
TGCCTCAGCAGCCACCCTCCCAGCAGCTGATGTCCAAGGGTCAGGACGAGCAAGAGGAGCTGGACTTCCTGTCTGACGAG
GAGATGGAGCAGATGGACGGGCAGAAGAACGCCTTCACTGCCTGGTCTGATGAGGACTCTGACTGTGAGATCGACGACCG
GGATGTCAACAAGATCCTCATCGTCACCCAGTCCCCACCTCACATGCGCAGGCACCCCGGCGGAGACCGCACAGGCAACT
GCACAGGCAGCCACACCTCGCATGCCAAGATGAGCGCCGAGCTGGCCAAGGTCATCGATGACGGCCTTTTCTACTACGAG
CAGGACCTGTGGACGGAGAAGTTCGAGCCTGAGTATTCC

Alignment

ORF - retro_tsyr_543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.04 %
• Parental protein coverage: 63.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRGRCRGGTRTHFDYQFGYRKFDGTEGPRTPKYMNNITYYFDNVSSTELYSVDQELLKDYIKRQIEYYFS
          GR.R.RGGTRTHF.YQFGYRKFDGTEGPRT.KYMNNIT..FDNVSSTELYSVDQELLKD..KRQ.EYYFS
Retrocopy GRDRGRGGTRTHFGYQFGYRKFDGTEGPRTSKYMNNITDCFDNVSSTELYSVDQELLKDHVKRQTEYYFS

Parental  VDNLERDFFLRRKMDADGFLP-ITLIASFHRVQALTTDLSLILMALKDSQVVEIVDEKVRRREEPEKWPL
          VD.LE.DFFLRRKMDADGFLP.ITL.ASFHR.QALTTD.SL...ALKDSQVVEIVDEKVRRREEPEKWPL
Retrocopy VDTLEPDFFLRRKMDADGFLP<ITLTASFHRGQALTTDISLLFAALKDSQVVEIVDEKVRRREEPEKWPL

Parental  PGPPIVDYSQTDFSQLLNXXXXXXXXXXXXXXXSAPGSPRAVTPVP-KTEEVSNLKTLRKGLSASLPDLD
          PGPPIVDYSQTDF.QLLN...............SAPGSPRA.TPVP.KTEEVSNLKTL.KGLSASLPDLD
Retrocopy PGPPIVDYSQTDFPQLLNCPEFVPC*HYQKETESAPGSPRAATPVPTKTEEVSNLKTLPKGLSASLPDLD

Parental  SENWIEVKKRPRPSPARPKKSEEPRFAHPASLPQQPPSQQLMSKDQDEQEELDFLFDEEMEQMDGRKNTF
          S..WIEVKKRPRPSPARPKKSEEPRFA.P.SLPQQPPSQQLMSK.QDEQEELDFL.DEEMEQMDG.KN.F
Retrocopy SKEWIEVKKRPRPSPARPKKSEEPRFARPTSLPQQPPSQQLMSKGQDEQEELDFLSDEEMEQMDGQKNAF

Parental  TAWSDEDSDYEIDDRDVNKILIVTQTPPYMRRHPGGDRTGN----HTSRAKMSAELAKVINDGLFYYEQD
          TAWSDEDSD.EIDDRDVNKILIVTQ.PP.MRRHPGGDRTGN....HTS.AKMSAELAKVI.DGLFYYEQD
Retrocopy TAWSDEDSDCEIDDRDVNKILIVTQSPPHMRRHPGGDRTGNCTGSHTSHAKMSAELAKVIDDGLFYYEQD

Parental  LWTEKFEPEYS
          LWTEKFEPEYS
Retrocopy LWTEKFEPEYS

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_543 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tarsius syrichta	ENSTSYG00000013732	1 retrocopy	retro_tsyr_543 ,