RetrogeneDB ID: retro_tbel_159

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1341:425012..425761(-)
• Located in intron of: ENSTBEG00000010710

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC47
• Ensembl ID: ENSTBEG00000009955
• Aliases: None
• Description: coiled-coil domain containing 47 [Source:HGNC Symbol;Acc:24856]

Sequence

>retro_tbel_159
CTGGCATGGATGATGAGGCCAGTGAGTGACCAAGTGCAAATCAGAGTGACCATGAATGATGAAGACATGGGTGCCTGTGT
GTTTGCTGTTGGCCACGGAAACCCTTGGTGCGATTGCAGAAGAAGATGCAAGATCTGAGTGAGTTTTGTAGTGCTAAACC
TAAGTCGGGAACCAAGTATGGACTGCCAGACTCCTTAGCTATCCTGTCAGAGATGAGAGAAGTCACTGAAGGAATGATGG
ATACCAAGATGGTTCACTTTCTCACACACTATGCCGACAAGATTGAATCTGTTCATTTTTCTGACCAGTTCTCTGGTCCA
AAAATGATGCAAAAGGAAGGTCAGCCTTTAAAACTGCCTGACACCAAGAAAACACTATTGTTTACATTTAATGTGCCAGG
CTCGGGTAACACCTACCCAAAGGATATGGAGGCCCTGCTACCCCTGATGAACATGGTGATTTATTCTATCGATAAAGCCA
GAAAGTTCCGACTCAACAGAGAAGGCAAACAAAAAGCAGATAAGAACCGTGCTCGAGTAGAGGAGAATTTCTTGAAGCTG
ACACATGAGCAAAGACAGGAAGCTGCACGGTCTCGACGTGAGGAGAACAAAAGAGCAGAGAAGGAGCGAATCCTGAACGA
AGAAGACCCTGAGAAGCAGCGCAGGCTGGAGGAAGCAGCTTTGAGGCACGAGCAGAAGAAGCTGGAGAAGAAGCAAATGA
AAATGAAACACGTCAAAGTGAAAGCCATG

Alignment

ORF - retro_tbel_159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.84 %
• Parental protein coverage: 51.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LARMMRPVSDQVQIKVTMNDEDMDTYVFAVG-TRKALVRLQKEMQDLSEFCSDKPKSGAKYGLPDSLAIL
          LA.MMRPVSDQVQI.VTMNDEDM...VFAVG..RK.LVRLQK.MQDLSEFCS.KPKSG.KYGLPDSLAIL
Retrocopy LAWMMRPVSDQVQIRVTMNDEDMGACVFAVG<PRKPLVRLQKKMQDLSEFCSAKPKSGTKYGLPDSLAIL

Parental  SEMGEVTEGMMDTKMVHFLTHYADKIESVHFSDQFSGPKIMQEEGQPLKLPDTKRTLLFTFNVPGSGNTY
          SEM.EVTEGMMDTKMVHFLTHYADKIESVHFSDQFSGPK.MQ.EGQPLKLPDTK.TLLFTFNVPGSGNTY
Retrocopy SEMREVTEGMMDTKMVHFLTHYADKIESVHFSDQFSGPKMMQKEGQPLKLPDTKKTLLFTFNVPGSGNTY

Parental  PKDMEALLPLMNMVIYSIDKAKKFRLNREGKQKADKNRARVEENFLKLTHVQRQEAAQSRREEKKRAEKE
          PKDMEALLPLMNMVIYSIDKA.KFRLNREGKQKADKNRARVEENFLKLTH.QRQEAA.SRREE.KRAEKE
Retrocopy PKDMEALLPLMNMVIYSIDKARKFRLNREGKQKADKNRARVEENFLKLTHEQRQEAARSRREENKRAEKE

Parental  RIMNEEDPEKQRRLEEAALRREQKKLEKKQMKMKQIKVKAM
          RI.NEEDPEKQRRLEEAALR.EQKKLEKKQMKMK..KVKAM
Retrocopy RILNEEDPEKQRRLEEAALRHEQKKLEKKQMKMKHVKVKAM

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_159 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_159 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000006869	1 retrocopy	retro_ogar_3092,
Rattus norvegicus	ENSRNOG00000009006	1 retrocopy	retro_rnor_2236,
Tupaia belangeri	ENSTBEG00000009955	1 retrocopy	retro_tbel_159 ,