RetrogeneDB ID: retro_tbel_2084

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_934:76003..76756(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL9
• Ensembl ID: ENSTBEG00000003816
• Aliases: None
• Description: methyltransferase like 9 [Source:HGNC Symbol;Acc:24586]

Sequence

>retro_tbel_2084
TGTGTGTAACAGAAATTATGTTAATCACGCCAGGCTGTCTTTGTTCAGAGTTACCTTGGTCAAGGAACACAGATCTCGAA
CAGCAGCATTGGGAAATCTAGCTGGCTATTTATCCAAATACATCATTCTTTTGTATCATCTGGTTTTAACTTGTTTATGT
CTAGAACAGCTATCAGTGGATTGCTAGGAAGAGGCTCATTTGTGTTTTCACCAGATCAGTTTCAGAGACTGCTTAAACTT
AACCCAGAGTGGAAAACCCATAGACTCCTTGATTCAGGTGCTGGAGACAGAGAAGTCACAAAAACCGTGAACCCTCATTT
TGAAGAAATCTATGCCACTGAACTTTCTGAAACTATGATATGACAACTTCAGAAGAAGAAATACGGAGTTCTTGGTATAA
ATGAATGGCAGAATACAGGGTTCCAATAAGATGTCATCAGCTGCTTGAATTTGATGGATTGCTATGACCAGCCTCTGACT
TTGTTAAAAGATAGAAGTGTCTGGAAGCCAATTAGAAGCCCGGTCGTCTTTGCCCTGGTCCTTCCCTTTCATCCCTATGT
GGAAGACAGTGACAAGTGTGAGAAACCATCAGAAATTTTGGAAATCAAGGGCCGGAATTGGAATTAACAAGTATATAGTC
TGCCTGAAGTTTTCAGAAAAGTTGGCTTTGTTATTGAAGCTTTCACCAGACTGCCATGCCTTTGTGAGGGTGACATATAT
AATGACTTCTATGTTCTGGATGCTGCATTGTTC

Alignment

ORF - retro_tbel_2084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 96.96 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWLFIQLYHSFVSSVFSLFMSRTSINGLLGRGSMFV
          C...KLC.S.QAVFVQSYL.QGTQI..N.SI.KS.WLFIQ..HSFVSS.F.LFMSRT.I.GLLGRGS.FV
Retrocopy CV*QKLC*SRQAVFVQSYLGQGTQIS-NSSIGKSSWLFIQIHHSFVSSGFNLFMSRTAISGLLGRGS-FV

Parental  FSPDQFQRLLKINPDWKTHRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGINEWQN
          FSPDQFQRLLK.NP.WKTHRLLD.GAGD.EVTK...PHFEEIYATELSETMI.QLQKKKY.VLGINEWQN
Retrocopy FSPDQFQRLLKLNPEWKTHRLLDSGAGDREVTKTVNPHFEEIYATELSETMI*QLQKKKYGVLGINEWQN

Parental  TGFQYDVISCLNLLDRCDQPLTLLKDIRSVLEPTRGRVILALVLPFHPYVENVGGKWEKPSEILEIKGQN
          TGFQ.DVISCLNL.D..DQPLTLLKD.RSV..P.R..V..ALVLPFHPYVE....K.EKPSEILEIKG.N
Retrocopy TGFQ*DVISCLNLMDCYDQPLTLLKD-RSVWKPIRSPVVFALVLPFHPYVED-SDKCEKPSEILEIKGRN

Parental  WEEQVNSLPEVFRKAGFVIEAFTRLPYLCEGDMYNDYYVLDDAVF
          W..QV.SLPEVFRK.GFVIEAFTRLP.LCEGD.YND.YVLD.A.F
Retrocopy WN*QVYSLPEVFRKVGFVIEAFTRLPCLCEGDIYNDFYVLDAALF

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_2084 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2084 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003533	2 retrocopies	retro_amel_402, retro_amel_704,
Canis familiaris	ENSCAFG00000017710	1 retrocopy	retro_cfam_1875,
Callithrix jacchus	ENSCJAG00000020564	1 retrocopy	retro_cjac_4083,
Mustela putorius furo	ENSMPUG00000016801	2 retrocopies	retro_mputfur_1323, retro_mputfur_1610,
Rattus norvegicus	ENSRNOG00000025940	1 retrocopy	retro_rnor_2623,
Sus scrofa	ENSSSCG00000030373	1 retrocopy	retro_sscr_441,
Tupaia belangeri	ENSTBEG00000003816	2 retrocopies	retro_tbel_1726, retro_tbel_2084 ,
Tursiops truncatus	ENSTTRG00000015624	4 retrocopies	retro_ttru_1100, retro_ttru_1466, retro_ttru_163, retro_ttru_467,