RetrogeneDB ID: retro_tbel_3677

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148229:3539..4598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACCSL
• Ensembl ID: ENSTBEG00000016623
• Aliases: None
• Description: 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like [Source:HGNC Symbol;Acc:34391]

Sequence

>retro_tbel_3677
ATGAGTCACAGGTCAGACACTTCCTCCATGTCCAGCAGCCCAACAAAGGGCCAGTTTCTCATGGGTCAGAGCATCTATGC
CCAGCTATTGAAGATGATGCAGCACTTGCAGCACATGGGGTGGGGGGATCATTTTGTACAATTGATAGCCTTGGGCATTC
AGCAGAGCCTGGCACTGGAAGGCCAGAATCACACTCAGGGCACCTGTTAGCCAGAAGCTCTCCTGGACTGCTTAATATAC
CAGATTATCAGTCTTCTACAGCGTGGGGCCATAGGTGGTCTGGGCCTCCAAGGACCTATCTGTTCCCCGGATACCAGGGA
TAATGTCAGAGGTGGGCAGAGGGCCCAATCACCTAGGCAGCCTGACCATCTAGCTTCCCAACTGTGTAATTATGAAGCTG
CATTTGTCAGCTATGACCTGTTCAACCATGGGATTGACATCTCTATCTTGTACCACTCGAGCTTCCAGGACTATGAAATT
TATCAGAGAAACAAATACCACAAGGGGGAAAGTACCTTGGGCATCATTAACCTTGGCACCAGTGAGAACAAGCTCTGCAC
TAATCTGATGACTGAAAGGTTCTGCCAGAGTGACATGAACTACATTGATAACACCCTTCTGCAATACTCTGATTGGAAAG
GCCAGCATTCCTGTGAGAAGATGTGGCCTGGTTCCTCACCTACTACTGTAAGGCACCTGTTCAATTTAATCTTGAAAATG
TGGTGGTTCTAAATGGCTACTCCTCTGTCTTCTCTGCACTGTCCATGGCTCTGAGTGACCCAGGAGAGGCCTTTTTGTTC
CATTCCCTTCTATGGTGGCTTCACTTTTAGTTCCCATCTATATGCAAAAGTTGAGCTGTTTCCTGTCCACCTGGAGAGTG
AGATCACTGATGCAAATAACTACCCTTTCCAGCTCACTGTGGACAAGTTGGAGCAAGCCTTGCTTGATACTAAACTTAAT
GAGAAAAAGGTCAGAGGCCTCGTGCTTATCAACCCTCAGAATCCTCTAGGTGACATCTCTTCCCGAGACTCTCTGAGGGA
CTACCTGGAATTTGTCAAA

Alignment

ORF - retro_tbel_3677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.87 %
• Parental protein coverage: 61.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHRSDTSSMPSGQTKGQVLMGQSIYTQLLKMMQHLQHMV-EDHFVQLTARRMEQSLALEDQSYTRAICK
          MSHRSDTSSM.S..TKGQ.LMGQSIY.QLLKMMQHLQHM...DHFVQL.A....QSLALE.Q..T...C.
Retrocopy MSHRSDTSSMSSSPTKGQFLMGQSIYAQLLKMMQHLQHMGWGDHFVQLIALGIQQSLALEGQNHTQGTC*

Parental  QEALLDRLIRQIIELLQSGATGGLGLRGPICSPDTRDDVRGGQRARSSRQPDHLASQLHNLEAAFINYDL
          .EALLD.LI.QII.LLQ.GA.GGLGL.GPICSPDTRD.VRGGQRA.S.RQPDHLASQL.N.EAAF..YDL
Retrocopy PEALLDCLIYQIISLLQRGAIGGLGLQGPICSPDTRDNVRGGQRAQSPRQPDHLASQLCNYEAAFVSYDL

Parental  SNRGVDISALYCSGFQDYETYQRSKYHEGENTLGFI-LGTSENKLCTDLMTERLCQSDMNYIDDALLQYS
          .N.G.DIS.LY.S.FQDYE.YQR.KYH.GE.TLG.I.LGTSENKLCT.LMTER.CQSDMNYID..LLQYS
Retrocopy FNHGIDISILYHSSFQDYEIYQRNKYHKGESTLGIINLGTSENKLCTNLMTERFCQSDMNYIDNTLLQYS

Parental  DFQGQ-PFLREEVARFLTYYCKAPAQLNPENVVVLNGCSSVFSALAMVLSDPGEAFL-VP-TPFYGGFAF
          D..GQ..FL.E.VA.FLTYYCKAP.Q.N.ENVVVLNG.SSVFSAL.M.LSDPGEAFL.VP..PFYGGF.F
Retrocopy DWKGQ<AFL*EDVAWFLTYYCKAPVQFNLENVVVLNGYSSVFSALSMALSDPGEAFL<VP<IPFYGGFTF

Parental  SSHLYAKVELFPVHLESEITDTNTHPFQLSVDKLEQALLDAKLDGKKVRGLVLINPQNPLGDIYSRDALK
          SSHLYAKVELFPVHLESEITD.N..PFQL.VDKLEQALLD.KL..KKVRGLVLINPQNPLGDI.SRD.L.
Retrocopy SSHLYAKVELFPVHLESEITDANNYPFQLTVDKLEQALLDTKLNEKKVRGLVLINPQNPLGDISSRDSLR

Parental  DYLEFAQ
          DYLEF..
Retrocopy DYLEFVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3677 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3677 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011384	1 retrocopy	retro_cjac_100,
Dipodomys ordii	ENSDORG00000005058	1 retrocopy	retro_dord_340,
Equus caballus	ENSECAG00000011908	1 retrocopy	retro_ecab_575,
Echinops telfairi	ENSETEG00000009026	2 retrocopies	retro_etel_1006, retro_etel_204,
Homo sapiens	ENSG00000205126	1 retrocopy	retro_hsap_3553,
Myotis lucifugus	ENSMLUG00000005151	1 retrocopy	retro_mluc_1235,
Nomascus leucogenys	ENSNLEG00000017966	1 retrocopy	retro_nleu_2326,
Ochotona princeps	ENSOPRG00000002097	1 retrocopy	retro_opri_526,
Ochotona princeps	ENSOPRG00000006805	7 retrocopies	retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252, retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii	ENSPPYG00000003340	1 retrocopy	retro_pabe_2934,
Pan troglodytes	ENSPTRG00000028662	1 retrocopy	retro_ptro_2414,
Tupaia belangeri	ENSTBEG00000016623	1 retrocopy	retro_tbel_3677 ,
Tursiops truncatus	ENSTTRG00000002727	1 retrocopy	retro_ttru_1321,