RetrogeneDB ID: retro_tsyr_1006

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_273840:374..1206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCKDHB
• Ensembl ID: ENSTSYG00000006573
• Aliases: None
• Description: branched chain keto acid dehydrogenase E1, beta polypeptide [Source:HGNC Symbol;Acc:987]

Sequence

>retro_tsyr_1006
GATCGGGTTTTTAATACTCCGTTGTGCGAACAAGGAATTGTTGGATTTGGAATCGGAATCGCCGTCACTGGTCCTACCGC
CGTTGCAGAAATTCAGTGTGCAGATGACATCTTTCCTGCTTTTGATCAGATTGTGAATGAAGCTGCCAAGTACGGCTACC
GCTCTAGGGCTCTTTTTAACTGTGGAAGCCTCACTATCCGGGCCCCTTGTTGGGGCTGTGTGGGCCCCCGGGCTCTCTAT
CATTCTCCGAGTCCCGAAGTTTTTTTTGGCTCATTGTCCAGGAATCAAGGTGGTTGTACCCAGAAGCCCTTTCCAGGCCA
AAGGACTTCTCTTGTCCTGCATAGAGGATAAAAATCCTTGTATATTTTTTGAACCTAAAATGCTTTACAGGGCAGCAGTG
GAACAAGTTCCGGTCGAGCCGTCCAGTATCCCACTGTCGCAGGCCGAAGTCATCCGGGAGGGGAGTGACGTCACTCTTGT
TGCCTGGGGCACCCAGGTTCATGGGGTTCGGGAAGTGGCTTCCATGGCAACAGAAAAGCTCGGCGTGTCTTGTGAAGTCA
TCGACCTGCGGACCATGTTACCTTGGGATGTGGACAGAGTTTGCAAGTCGGTGGCCAAGACCGGGCGGCTGCCGATCAGC
CACGAGGCTCCCCGGACCCGCGGCTTCGCGTGGGAGATCCAGCTCCACCGTGCAGGAAGAATGTTTCTGGAACCTGGAGG
CTCCTATGCCAAGAGTATGTGGGGCTGACACGCCGTTTCCTCACGTTTTCGAGTCATTCACATCCCAGACAAATGGAAGG
GTTACGAGGCCCTTCCAGAGATGATCAACTTT

Alignment

ORF - retro_tsyr_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 84.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DRVFNTLLCKQGIVGFGIRITVTGATAIAEIQFADYIFPAFDQIVNEAAKYRCHSGDLFNCGSLTIRAP-
          DRVFNT.LC.QGIVGFGI.I.VTG.TA.AEIQ.AD.IFPAFDQIVNEAAKY...S..LFNCGSLTIRAP.
Retrocopy DRVFNTPLCEQGIVGFGIGIAVTGPTAVAEIQCADDIFPAFDQIVNEAAKYGYRSRALFNCGSLTIRAPC

Parental  WGCVGHGAFYHSQSSEAFF-AHCPGIKVVVPRSPFQAKGLLLSCIEDKNPCIF-EPKILYRAAVEQVPVK
          WGCVG..A.YHS.S.E....AHCPGIKVVVPRSPFQAKGLLLSCIEDKNPCIF.EPK.LYRAAVEQVPV.
Retrocopy WGCVGPRALYHSPSPEXXX>AHCPGIKVVVPRSPFQAKGLLLSCIEDKNPCIFFEPKMLYRAAVEQVPVE

Parental  PYNIPLSQAKVIQEESDITLVAWGTQVHVVWEVTSMAKEKLGMSCEVINLRTILPWDVDTVCKSVAKTGR
          P..IPLSQA.VI.E.SD.TLVAWGTQVH.V.EV.SMA.EKLG.SCEVI.LRT.LPWDVD.VCKSVAKTGR
Retrocopy PSSIPLSQAEVIREGSDVTLVAWGTQVHGVREVASMATEKLGVSCEVIDLRTMLPWDVDRVCKSVAKTGR

Parental  LLISHEAPLTGGFASEI-SSTVQEECFLN-EYVVSRVCEYDTPFSHIFEPFC-IPDKWKCYDVLRKMINY
          L.ISHEAP.T.GFA.EI.SSTVQEECF.N.E....RVC..DTPF.H.FE.F..IPDKWK.Y..L..MIN.
Retrocopy LPISHEAPRTRGFAWEI>SSTVQEECFWNLEAPMPRVCGADTPFPHVFESFT<IPDKWKGYEALPEMINF

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_1006 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000000645	1 retrocopy	retro_ogar_1111,
Sus scrofa	ENSSSCG00000004465	1 retrocopy	retro_sscr_653,
Tarsius syrichta	ENSTSYG00000006573	1 retrocopy	retro_tsyr_1006 ,